Plant Chromosome Biology
Cytogenetics meeting 2023

Book of abstracts

September 11-13, Brno

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Plant Chromosome Biology: Cytogenetics meeting 2023

September 11-13, 2023, Brno

Plant Chromosome Biology
Cytogenetics meeting 2023
September 11-13, Brno

The conference brings together researchers investigating all aspects of plant genomes.
Considering the ongoing progress in the field of chromosome biology, the focus of thismeeting will be the structure of plant chromosomes and genome dynamics in the lightof epigenomic stability. The program addresses a broad spectrum of fundamental andapplied aspects of these topics.
Like the years before, the meeting provides excellent opportunities to stimulatescientific discussions regarding chromosome engineering, advanced chromosome
biology and plant breeding.
Organizers:
Roman Hobza, Department of Plant Developmental Genetics, Institute of Biophysics
of the Czech Academy of Sciences
Andreas Houben, Society for Plant Breeding e.V. (GPZ), section “Cytogenetic andChromosome Analysis”.

1Plant Chromosome Biology: Cytogenetics meeting 2023

September 11-13, 2023, Brno

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2

Plant Chromosome Biology: Cytogenetics meeting 2023

September 11, 2023, Brno

Programme
11 September 2023:
8:00 - 8:30:
Registration
8:30 - 9:00:
Opening ceremony
9:00 - 10:25:
Session 1: Genome stability, nucleus and chromosome architecture
10:25 - 10:50:
Coffee Break
10:50 - 12:10:
Session 1: Genome stability, nucleus and chromosome architecture
12:10 - 12:30:
Session 1: Poster pitches
12:30 - 13:20:
Lunch
13:20 – 13:40: Partners presentations
13:40 - 14:45:
Session 2: Genome and chromosome evolution, environmental response and plasticity
14:45 – 15:10:
Coffee break
15:10 - 16:10:
Session 2: Genome and chromosome evolution, environmental response and plasticity
16:10 – 16:40:
Session 2: Poster pitches
16:40 – 16:55:
Break
16:55 – 18:40:
Session 3: New tools, perspectives and applications
18:40 – 19:00:
Session 3: Poster pitches
19:00:
Posters Dinner (Session 1, 2, 3)
3

Plant Chromosome Biology: Cytogenetics meeting 2023

September 12-13, 2023, Brno

12 September 2023:
08:30 - 09:55:
Session 4: Mitosis, meiosis, gamete formation, polyploidy and apomixes
09:55 - 10:15:
Coffee break
10:15 - 11:30:
Session 4: Mitosis, meiosis, gamete formation, polyploidy and apomixes
11:30 - 11:40:
Session 4: Poster pitches
11:40 - 12:40:
Coffee + Posters (Session 4)
12:40 - 13:30:
Lunch
13:40:
Departure to the Mendel Museum
13:50 - 14:20:
Eva Chocholová: Peas of Mendel´s life revealed by dental calculus
14:20 - 14:50:
Ingo Schubert: The fate of Mendel's discoveries
15:00 - 18:00:
Tours of the Mendel Museum / free time
18:00:
Conference Dinner
13 September 2023:
8:30 - 10:05:
Session 5: Specialized chromosomes (Sex chromosomes, B chromosomes and others)
10:05 – 10:20
Session 5: Poster pitches
10:20-10:40:
Andreas Houben: Plant chromosome biology - Quo vadis?
10:40 – 11:40: Coffee + Posters (Session 5)
11:40 - 12:10:
Awards and closing ceremony
12:10:
Lunch
4

Plant Chromosome Biology: Cytogenetics meeting 2023

September 11, 2023, Brno

List of talks
Session 1:
Time:
Chair:
1. Mainspeaker:
2. Talk

3. Talk

4. Talk

5. Talk
6. Talk

7. Talk

Poster pitch
session for
poster:

Genome stability, nucleus and chromosome architecture
2 hours and 45 minutes
Hana Šimková and Jiří Fajkus
Holger Puchta: Applying
Abstract 1
9:00 – 9:45
CRISPR/Cas to plants: Fromgene editing to chromosome
engineering
Takayoshi Ishii: Chromosome
Abstract 2
9:45 – 10:05
elimination during hybrid
embryogenesis of Poaceae:
wheat/oat × PennisetumJiří Fajkus: Telomerase RNA
Abstract 3
10:05 – 10:25
gene paralogs: the usual
pathway to unusual plant
telomeres
Yi-Tzu Kuo: Mitotic and
Abstract 4
10:50 – 11:10
meiotic centromere dynamics
diﬀer in a holocentric species
with megabase-sizedcentromere units
Paula Franke: Key aspects of
Abstract 5
11:10 – 11:30
the spatial nucleus organizationin the Brachypodium genus
István Molnár: U
Abstract 6
11:30 – 11:50
chromosomes of Aegilops
biuncialis are more frequently
eliminated than M
chromosomes during theirintrogression into wheat
Mehrdad Shahbazi:
Abstract 7
11:50 – 12:10
Cytonuclear Interactions in
Auto- and Allopolyploids of
Festuca-Lolium Complex
8, 9, 10, 11, 12, 13, 14, 15

5Plant Chromosome Biology: Cytogenetics meeting 2023

September 11, 2023, Brno

List of talks
Session 2:

Genome and chromosome evolution, environmental response
and plasticity
Time:
2 hours and 5 minutes
Chair:
Martin Lysák and Ingo Schubert
1. MainTony Heitkam: The Crocus
Abstract 16
13:40 – 14:05
speaker: Chronicles: Decoding the
Triploid Puzzle of Clonal
Saffron Crocus
2. Talk
Sreetama Bhadra: The impact
Abstract 17
14:05 – 14:25
of genome size on trait
ﬂexibility, evolutionary
radiation and the distribution ofangiosperms
3. Talk
Bozena Kolano: Evolutionary
Abstract 18
14:25 – 14:45
Dynamics of tandem repetitive
sequences in Crepis sensu lato
4. Talk
Terezie Mandáková: Origin and Abstract 19
15:10 – 15:30
evolution of diploid andallopolyploid Camelina
genomes
5. Talk
Hanna Weiss-Schneeweiss:
Abstract 20
15:30 – 15:50
Prospero’s magic: when
karyotypic and genomicchanges drive diversiﬁcation(and the phenotype does notkeep up)
6. Talk
Trude Schwarzacher: Insights
Abstract 21
15:50 – 16:10
into chromosome and repetitive
sequence evolution in
Musaceae from long-molecule,t2t genome assemblies andmolecular cytogenetics
Poster pitch
session for
22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34
poster:6

Plant Chromosome Biology: Cytogenetics meeting 2023

September 11, 2023, Brno

List of talks
Session 3:
Time:
Chair:
1. Mainspeaker:
2. Talk
3. Talk
4. Talk

5. Talk

Poster pitch
session for
poster:New tools, perspectives and applications
1 hours and 45 minutesJiří Macas and Jan Bartoš
Jaroslav Doležel: Let them
Abstract 35
move: ﬂow cytometricchromosome analysis andsorting
Hana Šimková: A 3C view of 3D Abstract 36
genome dynamics in barley
Petr Novák: RepeatExplorer
Abstract 37
tools for genome annotations
Nobuko Ohmido: Unveiling the Abstract 38
Nano-World of Plant
Chromosomes: Chromatin Fiber
Compaction and Scaﬀold
Protein Localization using
Advanced Microscopy
Techniques
Takashi Okamoto: Wheat-rice
Abstract 39
hybrid mitochondria in
Oryzawheat and theirtransmission to the next
generation

16:55 – 17:20

17:20 – 17:40
17:40 – 18:00
18:00 – 18:20

18:20 – 18:40

40, 41, 42, 43, 44, 45

7Plant Chromosome Biology: Cytogenetics meeting 2023

September 12, 2023, Brno

List of talks
Session 4:
Time:
Chair:
1. Mainspeaker:
2. Talk

3. Talk
4. Talk

5. Talk
6. Talk

7. Talk

8. Talk

Poster pitch
session for
poster:Mitosis, meiosis, gamete formation, polyploidy and apomixes
2 hour and 40 minutes
Andreas Houben and Miroslava Karafiátová
Jiri Macas: Comparative
Abstract 46
8:30 – 8:55
genomics of plant centromeres
Begoña Quirós-de-la-Peña:
Abstract 47
8:55 – 9:15
Cytogenetic and molecularevidence for polyclonality andsexual events in allopolyploidapomictic species Hieracium
halleri (Asteraceae)
Ales Pecinka: Spatial in vivo
Abstract 48
9:15 – 9:35
dynamics of mitotic divisions inbarley (Hordeum vulgare)Jana Lunerová, Veit Herklotz:
Abstract 49
9:35 – 9:55
Unraveling the Rosa canina
Genome: Cytogenetic,
Genomic, and Phylogenetic
Insights into Pentaploid
Genome Harbouring
Asymmetrical Meiosis.
Inna Lermontova: The protein- Abstract 50
10:15 – 10:35
protein interaction network of
KNL2 in Arabidopsis thaliana
Suriya Tamilselvan Nattar
Abstract 51
10:35 – 10:55
Amutha: Single pollen nucleus
genotyping and virus tools formeiotic gene studies in barley(Hordeum vulgare L.)
Stefan Steckenborn: Dynamics Abstract 52
10:55 – 11:15
and adaptation of the meiotic
recombination landscapeamong natural and artiﬁcial
chromosomes in holocentric
Rhynchospora plant species
Veronika Kolačková: STED
Abstract 53
11:15 – 11:30
nanoscopy of intra-nuclear
chromatin structures in barley(Hordeum vulgare L.)54, 55, 56, 57, 58, 59, 60, 61, 62

8Plant Chromosome Biology: Cytogenetics meeting 2023

September 13, 2023, Brno

List of talks
Session 5:
Time:
Chair:
1. Mainspeaker:
2. Talk
3. Talk

4. Talk

5. Talk
Poster pitch
session for
poster:Closing talkSpecialized chromosomes (Sex chromosomes, B chromosomes
and others)
1 hour and 55minutes
Roman Hobza and Sònia Garcia
Roman Hobza: Key drivers of
Abstract 63
8:30 – 8:50
plant sex chromosomes
knowledge explosion
Václav Bačovský: A complex
Abstract 64
8:50 – 9:10
aﬀair – sex chromosome
evolution in plants
Lucie Horáková: Considerable
Abstract 65
9:10 – 9:25
genetic diversity within the hop
varieties explains nonMendelian segregation patterns
Miroslava Karaﬁátová: Does B Abstract 66
9:25 – 9:45
chromosome alternate thepollen development in wildsorghum?
Sònia Garcia: Unveiling
Abstract 67
9:45 – 10:05
Reproductive Diversity: Tree ofSex 2.0 Progress Report69, 70, 71, 72, 73, 74, 75, 76
Andreas Houben: Plant
chromosome biology - Quovadis?

Abstract 68

10:20 – 10:40

9

Plant Chromosome Biology: Cytogenetics meeting 2023

September 11, 2023, Brno

List of posters
Session 1:
1.
2.
3.
4.
5.
6.
7.
8.

Genome stability, nucleus and chromosome architecture
Eszter Gaál: Crested wheatgrass and the
Abstract 8
gametocidal genes system to widen the gene poolof wheat
Anna Nowicka: Towards an understanding of
Abstract 9
nuclear morphology and chromosome organizationin endoreduplicated nuclei of barley seed tissuesOndřej Helia: Eﬀects of extensive chromosomal
Abstract 10
rearrangements in terms of genetics andepigenetics in Arabidopsis thaliana model plantAlžběta Doležalová: Variability in mutual
Abstract 11
chromosome positioning in 3D space of rice nuclei
Solmaz Khosravi: Chromosomal rearrangments and Abstract 12
epigenetic consequences
Marcel Hubinský: Extensive chromosomal changes
Abstract 13
and seed geometric morphometrics in Silene
Eva Sýkorová: Chromosomes at their ends –Abstract 14
evolutionary perspectives

Serhii Mykhailyk: Nucleolar dominance in theallotetraploid model grass Brachypodium hybridum– exploring molecular mechanisms behind thecytogenetic phenomenon.

Abstract 15

10Plant Chromosome Biology: Cytogenetics meeting 2023

September 11, 2023, Brno

List of posters
Session 2:
1.
2.

3.
4.
5.

6.

7.
8.
9.
10.
11.
12.

Genome/Chromosome evolution, environmental response andplasticity
Nomar Waminal: Dysploidy in spring crocuses
Abstract 22(Crocus series Verni)
Yile Huang: The pathways of whole-genome
Abstract 23
duplications, diploidization, and descending
dysploidy in the Biscutelleae (Brassicaceae)
Hina Shimomai: Urban environments,
chromosome formula and polyploidization in two
Commelina species
Sara Ishiguro: Major genotype-panels for
Hydrangea genomics by comparative repeat
analysis
Xinyi Guo: The ampliﬁcation of interstitial
telomeric repeats accompanied genome
evolution in the East Asian genus Yinshania(Brassicaceae)
Dana Trunova: Does the time matter? Revealing
the pathways of rRNA gene evolutionin
Brachypodium hybridum of diﬀerent
evolutionary age.
Jana Čížková: Evolution of the family Musaceae
through large chromosomal rearrangements
Anton Stepanenko: Nucleotide level structure of
5S rDNA loci in the great duckweed, Spirodela
polyrhiza
Sophie Maiwald: Evolving together: Cassandra
retrotransposons gradually mirror promoter
mutations of the 5S rRNA genes
Milan Pouch: Polyploidy-driven genome
evolution of the South African genus Heliophila(Brassicaceae)
Thiago Nascimento: Independent and recurrent
dysploidy events in Phaseolus beans
Nicola Schmidt: Repeat turnover meets stable
chromosomes: Repetitive DNAs mark speciationand gene pool boundaries in sugar beet and wild
beets

Abstract 24
Abstract 25
Abstract 26

Abstract 27

Abstract 29
Abstract 30
Abstract 31
Abstract 32
Abstract 33
Abstract 34

11Plant Chromosome Biology: Cytogenetics meeting 2023

September 11, 2023, Brno

List of posters
Session 3:
1.

2.
3.
4.
5.
6.

New tools, perspectives and applications
Tereza Šlajsová: The application laboratory for
agricultural research at the Centre of Plant
Structural and Functional Genomics of Institute ofExperimental BotanyPetr Fajkus: Computational identiﬁcation ofevolutionary conserved non-coding RNAs
Martina Nešpor Dadejová: Detection of protein
recruitment and protein-protein interactions at
DNA lesions in plant protoplasts
Ludwig Mann: High-ﬁdelity repeat consensus
sequences from short reads
Bhanu Prakash Potlapalli: Development of novel
CRISPR/Cas9-based tools for visualizing genomic
sequences
Petr Janás: Reversing ancient chromosomal
rearrangements in Cardamine hirsuta(Brassicaceae) using CRISPR/Cas

Abstract 40

Abstract 41
Abstract 42
Abstract 43
Abstract 44
Abstract 45

12Plant Chromosome Biology: Cytogenetics meeting 2023

September 12, 2023, Brno

List of posters
Session 4:
1.

2.
3.
4.
5.
6.
7.
8.

9.

Mitosis, Meiosis, gamete formation, polyploidy and apomixes
Jana Szecówka: Both male and female meiosis
Abstract 54
contribute to non-Mendelian inheritance ofparental chromosomes in interspecific planthybrids (Lolium × Festuca)
Azahara C. Martin: ZIP4 is required for normal
Abstract 55
progression of synapsis and for over 95% ofcrossovers in wheat
Astrid Johanna Irena Severyns: Uncovering the
Abstract 56
mechanism of cold-induced meiotic restitution inMusa spp.
Ramakrishna Yadala: Recurrent plant-speciﬁc
Abstract 57
duplications of KNL2 and its conserved function
as a kinetochore assembly factor
Baicui Wang: Identiﬁcation of novel meiotic
Abstract 58
players based on screening of Axis TurboID
candidates (ATC) and SUMO candidates
Maria Cuacos: Anti- and pro-CO factors in
Abstract 59barleyZhenling lyu: Tetraploid B. rapa are highly
Abstract 60
tolerant of tetravalent formation and aneuploidy
Ludmila Oliveira: Antibodies against kinetochore Abstract 61
proteins NDC80 and KNL1 provide highly
versatile markers of centromeres in ﬂowering
plants (angiosperms)
Chao Feng: Proteomic proﬁling of meiotic
Abstract 62
chromosome axis in Arabidopsis thaliana basedon TurboID

13

Plant Chromosome Biology: Cytogenetics meeting 2023

September 13, 2023, Brno

List of posters
Session 5:
1.
2.
3.

4.
5.
6.
7.
8.
9.

Specialized chromosomes (Sex chromosomes, B chromosomes
and others)
Jana Kružlicová: Weird and wonderful – an origin
Abstract 69
of sex chromosomes in two races of Rumex
hastatulus
Jianyong Chen: Identiﬁcation of the trans-acting
Abstract 70
factors that control the non-Mendelian drive of therye B chromosome
Gihwan Kim: Identiﬁcation and functional
Abstract 71
characterization of genes controlling the process ofroot-speciﬁc B chromosome elimination in Aegilops
speltoides
Pavla Novotná: Dosage compensation mechanism
Abstract 72
in plants with evolutionary young sex chromosomes
Lucie Hloušková: Characterization of a maize
Abstract 73
landraces collection concerning the B chromosome
Joan Pere Pascual-Díaz: Sex-chrome version 2.0: a Abstract 74
database of green plant species with sex
chromosomes
Marcel Hubinský: Non canonical bases as possible
Abstract 75
regulators of sex chromosomes in the dioecious
plant Silene latifolia
Pavel Jedlička: Extended reconstruction of
Abstract 76
transposable elements in plants using TE-greedynester
Kashif Nawaz: Assembly of saltgrass genomes
Abstract 78
reveals unique genomic features of a dioecious,
perennial, halophytic grass

14

Plant Chromosome Biology: Cytogenetics meeting 2023

September 11, 9:00-12:10

Session 1
Genome stability, nucleus and chromosome
architecture
Talks

15

Plant Chromosome Biology: Cytogenetics meeting 2023

Session 1, Talk, 9:00-9:45

1.

Applying CRISPR/Cas to plants: From gene editing tochromosome engineering
Holger Puchta1
1. Joseph Gottlieb Kölreuter Institute for Plant Sciences, Karlsruhe Institute ofTechnology

Till today programmable nucleases as CRISPR/Cas have been applied to plants mainly
on genes for the improvement of traits. However, breeding also requires the breaking
or establishing genetic linkages on the chromosome level. Using Cas9, we were able tochange genetic linkages by inducing heritable translocations in the Mb range between
heterologous chromosomes in Arabidopsis thaliana. Recent improvements in sequence
analysis of crop plants reveal that multi Mb long inversions occur with high frequency
between diﬀerent genotypes, leading to crossover suppression. We were not only able
to demonstrate that inversions up to almost chromosome size can be achieved in
Arabidopsis, but also meiotic recombination can be redirected this way. Thus, on one
side a recombination dead region could be reactivated after 5000 years and on theother almost a complete chromosome could be excluded from genetic exchange. In the
future, CRISPR/Cas-mediated chromosomal engineering will allow us to restructure
plant genomes according to our needs for breeding. Finally, we developed a newtechnology based on DSB-induced genome elimination for tissue engineering named
CRISPR-Kill, allowing us to induce targeted cell death in diﬀerent organs at selectdevelopmental stages. Recently we were able to set up an inducible CRISPR-Kill system,
allowing also the temporal control of cell death.

16Plant Chromosome Biology: Cytogenetics meeting 2023

Session 1, Talk, 9:45-10:05

2.
Chromosome elimination during hybrid embryogenesis of
Poaceae: wheat/oat × Pennisetum
Takayoshi Ishii1
1. Arid Land Research Center, Tottori University
Wide hybridisation is one of the practical methods for increasing genetic diversity inplant breeding. However, there are several levels of incompatibility during wide
hybridisation in diﬀerent species combinations. Wheat (Triticum aestivum) can crosswith subfamilies of distant species such as maize (Zea mays), sorghum (Sorghum bicolor)and pearl millet (Pennisetum glaucum). Sperm from these species fertilise the wheat egg.
However, non-wheat chromosomes are eliminated during early embryogenesis. In theoat (Avena sativa) x pearl millet combination, all the pearl millet chromosomes are
retained in the background of the haploid oat genome during embryogenesis and young
seedling formation. Maternal and paternal factors inﬂuence chromosome elimination.
To elucidate the paternal factors inﬂuencing the process of chromosome elimination,
we crossed several diﬀerent Pennisetum species with wheat and oat. Diﬀerent degrees
of chromosome elimination were found. 1. rapid chromosome elimination, 2. gradualchromosome elimination, 3. retention of a few chromosomes and 4. no chromosome
elimination.

17

Plant Chromosome Biology: Cytogenetics meeting 2023

Session 1, Talk, 10:05-10:25

3.
Telomerase RNA gene paralogs: the usual pathway tounusual plant telomeresMgr. Petr Fajkus, Ph.D.1, Mgr. Michal Závodník2, Mgr. Vratislav Peška, Ph.D.3, Prof.
RNDr. Jiří Fajkus, Ph.D.4
1. Institute of Biophysics ASCR, and Masaryk University, CEITEC
2. Masaryk University, CEITEC, and Faculty of Science, NCBR
3. Institute of Biophysics, ASCR
4. Masaryk University, CEITEC, Masaryk University, Faculty of Science, NCBR, andInstitute of Biophysics, ASCR.
Telomerase, telomere DNA and associated proteins represent a complex, ﬁnely tuned,and functionally conserved mechanism that ensures genome integrity by protecting andmaintaining chromosome ends. Changes of its components can threaten an organism’s
viability. Nevertheless, molecular innovation in telomere maintenance has occurredmultiple times during eukaryote evolution, giving rise to species/taxa with unusual
telomeric DNA sequences, telomerase components, or telomerase-independent
telomere maintenance. The central component of telomere maintenance machinery is
telomerase RNA (TR) as it templates telomere DNA synthesis, its mutation can change
telomere DNA and disrupt its recognition by telomere proteins, thereby leading tocollapse of their end-protective and telomerase recruitment functions. Using a
combination of bioinformatic and experimental approaches, we examine a plausible
scenario of evolutionary changes in TR underlying telomere transitions. We identiﬁed
plants harbouring multiple TR paralogs whose template regions could support thesynthesis of diverse telomeres. In our hypothesis, formation of unusual telomeres is
associated with the emergence and occurrence of TR paralogs that can accumulate
mutations, and through their functional redundancy, allow for the adaptive evolutionof the other telomere components. Experimental analyses of telomeres and telomerasein the examined plants demonstrate evolutionary telomere transitions corresponding
to TR paralogs with diverse template regions.

18Plant Chromosome Biology: Cytogenetics meeting 2023

Session 1, Talk, 10:50-11:10

4.
Mitotic and meiotic centromere dynamics differ in a
holocentric species with megabase-sized centromere units
Yi-Tzu Kuo1, Amanda Souza Câmara1, Veit Schubert1, Pavel Neumann2, Jiří Macas2,
Jianyong Chen1, Michael Melzer1, Jörg Fuchs1, Takayoshi Ishii3, André Marques4,
Andreas Houben1
1. Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben,
Germany
2. Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology,České Budějovice, Cezch Republic
3. Tottori University, Arid Land Research Center, Tottori, Japan
4. Department of Chromosome Biology, Max Planck Institute for Plant Breeding
Research, Cologne, Germany
The centromere is the chromosomal region where the spindle microtubules attachduring cell division. In contrast to monocentric chromosomes with a single centromere
location in most known species, holocentric species exist with a centromere distributed
throughout chromosome length. The mechanism that triggered a centromere-typetransition might diﬀer among independently evolved holocentric lineages, leading todiverse holocentromere compositions. We found a drastic change in centromere
organization
betweenthe closely related
monocentric Chamaelirium andholocentric Chionographis. Remarkably, in Chionographis japonica, the repeat-based
holocentromere is formed based on only a few monocentromere-like megabased-sizedcentromere units. The composition and distribution of the centromere units inﬂuenced
the large-scale genome organization and formed distinct eu- and heterochromatic
domains. The genome organization in Chionographis possesses characteristics of bothmonocentric and holocentric species, distinct from those in other known holocentric
species. Additionally, Chionographis performs a monocentromere-like meiosis, in which
the multiple centromere units of each chromatid form a single cluster and act like a
monocentromere. Strikingly, the sister centromeres are unfused at meiosis I, resulting
in four centromere clusters on each bivalent. Our ﬁndings broaden the knowledge
about the diversity of centromere organizations. We demonstrate the unique value ofanalyzing non-model species for evolutionary comparisons to reveal novelties in evenwell-studied structures.

19Plant Chromosome Biology: Cytogenetics meeting 2023

Session 1, Talk, 11:10-11:30

5.
Key aspects of the spatial nucleus organization in
the Brachypodium genus
MSc Paula Franke1, MSc Chinedum Anajemba1, dr Manoj Kumar Solanki1, dr JoannaŁusińska1, dr Ewa Robaszkiewicz1, dr Artur Piński1, dr Elżbieta Wolny1, dr Dominika
Idziak-Helmcke1, prof. Robert Hasterok1
1. Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology
and Environmental Protection, Faculty of Natural Sciences, University of Silesia in
Katowice, 28 Jagiellonska Street, 40-032 Katowice, Poland
The 3-D arrangement of interphase chromatin greatly impacts the processes in the
nucleus and the organism. Small-genome grass species of the Brachypodium genus areused as models for studying diﬀerent aspects of chromatin spatial arrangement inplants. Our ongoing studies use 3-D ﬂuorescence in situ hybridization (FISH) on isolated
leaf and root nuclei of various Brachypodium species to address diploid and polyploid
genome organization diﬀerences and the role of diﬀerent nuclear envelope proteins inpreserving 3-D chromatin structure.
Preliminary analysis of parental subgenome positioning in an allotetraploid B.
hybridum interphase nuclei with the use of subgenome-speciﬁc BAC clones showedthat parental subgenomes predominantly occupy distinct nuclear territories, with only
little intermingling at the territories’ borders. The position and the size of the territories
have been characterized.
Analysis of centromeric and telomeric domain number and distribution by FISH in
diﬀerent genotypes of Brachypodium species indicated intraspeciﬁc variation in domain
association. A similar analysis performed on B. distachyon SUN2 knock-out mutant
suggests that lack of SUN2 envelope protein may also aﬀect speciﬁc domain
arrangement in the nucleus.
The authors acknowledge ﬁnancial support from the National Science Centre, Poland(grant no. 2018/31/B/NZ3/01761).

20

Plant Chromosome Biology: Cytogenetics meeting 2023

Session 1, Talk, 11:30-11:50

6.
U chromosomes of Aegilops biuncialis are more frequently
eliminated than M chromosomes during their introgression
into wheat
István Molnár1, Eszter Gaál1, András Farkas1, László Ivanizs1, Balázs Kalapos1, Edina
Türkösi1, Klaudia Kruppa1, Éva Szakács1, Mahmoud Said2, Abraham Korol3, Jaroslav
Doležel2, Miroslav Valárik2
1. Department of Biological Resources, Centre for Agricultural Research, Eötvös Lóránd
Research Network, 2462, Hungary
2. Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant
Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech
Republic
3. Institute of Evolution and Department of Evolutionary and Environmental Biology,
University of Haifa, 199 Aba Khoushy Ave., Mount Carmel, Haifa 3498838, Israel
Wild goatgrass, Aegilops biuncialis (UbUbMbMb) represents an untapped source ofgenetic diversity that could be exploited in wheat improvement. However, chromosome
mediated gene introgression from wild relatives into wheat has been hampered by thelack of genome reﬀerence sequence and scarcity of molecular tools.
A DArTseq genetic map of F2 populationderived from cross of Ae. biuncialis MvGB642
x MvGB382 lines revealed well preserved collinearity of the Mb-genome with breadwheat, while multiple karyotype reconstructions were identiﬁed in the Ub-genome. The
wheat-Aegilops synteny allowed mapping of the DArTseq markers in a wheat x Ae.
biuncialis BC3F1-3 population. The DArTseq genotyping in combination withﬂuorescence in situ hybridization (FISH) using U- and M-genomic- and DNA and Afa
family, pSc119.2 and 45S rDNA repetitive probes conﬁrmed the presence of Ae.
biuncialis chromosomes 1MbS, 3Mb, 4Mb, 5Mb and 6Mb, while a majority of
Ub chromosomes was lost and only 1Ub-, 2Ub-, 4Ub- and 7Ub chromosomal fragments
were present in some lines. The new addition-, substitution and introgression lines
together with the chromosome speciﬁc markers will facilitate development of new
wheat cultivars adapted to the changing environmental conditions.
This work has been supported by ERDF project ‘Plants as a tool for sustainable global
development’ (No. CZ.02.1.01/0.0/0.0/16_019/0000827) and the Hungarian National
Research, Development and Innovation Oﬃce (K135057; TKP2021-NKTA-06).

21

Plant Chromosome Biology: Cytogenetics meeting 2023

Session 1, Talk, 11:50-12:10

7.
Cytonuclear Interactions in Auto- andAllopolyploidsof Festuca-Lolium Complex
Mehrdad SHAHBAZI1, Jana SZECÓWKA1, Denisa KUBÍKOVÁ1, Joanna MAJKA1, DavidKOPECKÝ1
1. Institute of Experimental Botany, CAS
Some Protein complexes consist of both nuclear and organellar-encoded subunits. For
example, the large subunit of Rubisco is encoded by the plastid gene RbcL, while thesmall subunit is encoded by the nuclear gene RbcS. The subunits of such protein
complexes are interdependent and precisely regulated at the genomic, transcriptomic,
and post-transcriptomic levels. The stoichiometry between the subunits and theiroptimal assembly can be disrupted by polyploidization, which increases the ploidy levelof the nuclear genome without instant doubling of the organellar genome, andhybridization, which merges two distinct genomes. In this study, we investigate boththe stoichiometry restoration mechanisms of Festuca prantesis and Lolium multiﬂurom
autopolyploids and conﬂicts in genomics, transcriptomics, and structural proteomics
resulting from merging two genomes in allopolyploids (with maternally inheritedorganellar genomes). Our data suggest that increasing chloroplast number andespecially chloroplastic gene copy number in autopolyploids are the main contributors
to stoichiometry restoration without signiﬁcant changes in gene expression level. In
allopolyploids, we detected that although the chloroplast genome is inherited strictly
maternally, the majority of the nuclear genes involved in cytonuclear complexes are
expressed equally from both homoeologues, with the exception of PSB domain 7(PPD7), which was mainly expressed from Lolium multiﬂurom. Diﬀerences in the aminoacid composition between the homoeologues did not signiﬁcantly alter the binding site
structure or the electrostatic potential of the surface except in the PPD7 protein, in
which substitution of isoleucine (I) with L-threonine (T) can contribute to potential
diﬀerences in protein stability and hydrogen bonding interactions.

22Plant Chromosome Biology: Cytogenetics meeting 2023

Session 1, Posters, September 11

Session 1
Genome stability, nucleus and chromosome
architecture
Posters23

Plant Chromosome Biology: Cytogenetics meeting 2023

Session 1, Posters, September 118.
Crested wheatgrass and the gametocidal genes system towiden the gene pool of wheat
Eszter Gaál, PhD1, MSc. Mahmoud Said, PhD2, Prof. Adoración Cabrera, DrSc.3, Éva
Szakács, PhD1, András Farkas, PhD1, László Ivanizs, PhD1, Edina Türkösi, PhD1, Prof.
Takashi Endo, DrSc.4, Prof. Ing. Jaroslav Doležel, DrSc.2, István Molnár, DrSc.1
1. Agricultural Institute, Centre for Agricultural Research, Martonvásár, Hungary
2. Institute of Experimental Botany of the Czech Academy of Sciences
3. Genetics Department, ETSIAM, University of Córdoba, Spain
4. Faculty of Agriculture, Ryukoku University, Japan
Gene pool of wheat has narrowed during domestication and cultivation over thousands ofyears. Wild relatives of wheat are promising source of new genes for wheat improvement.
Crested wheatgrass (Agropyron cristatum L. Gaertn.) represents a rich source of important
genes. Gametocidal (Gc) system is an eﬃcient approach to transfer useful traits to wheat fromwild relatives. Gc genes induce chromosomal rearrangements in gametes lacking them inmonosomic addition of the Gc chromosome. The utilization of wild genetic diversity has beenhampered by low throughput of selection methods and the lack of knowledge on genomes ofwild relatives. Conserved Ortholog Set (COS) markers speciﬁc for genes conserved throughout
evolution deﬁne orthologous regions, thus enabling comparison of regions on chromosomes ofrelated species.
We crossed wheat Chinese Spring (CS)-A. cristatum 5P and 6P chromosome addition lines with
CS-Ae. cylindrica 2C chromosome addition line with Gc eﬀect to induce structural
rearrangements between wheat and 5P or 6P chromosomes. GISH and FISH analysis of
BC1F2 detected seven and two wheat-Agropyron translocations for 5P and 6P, respectively.
Three 5P-wheat and one wheat-6P translocations were transferred to the next generation.
Characterization of selfed progenies indicated that 5P introgressions positively aﬀected grain
number per plant. We also used fourteen wheat–A. cristatum disomic and ditelosomic additions
and the 1PS·1BL translocation line to map COS markers on Agropyron and to characterizesyntenic relationships. Out of 328 selected COS markers, 279 consistently ampliﬁed products
in tetraploid A. cristatum, and, out of these, 139 were polymorphic between tetraploid crested
wheatgrass and wheat. Sixty-nine markers were found to be suitable for the detection oftetraploid A. cristatum chromosomes 1P–6P in wheat, ranging from 6 to 17 markers per
chromosome. Generally, markers of the same homeologous group were detected on the same
chromosome arms.
Acknowledgments:
This research was funded by the Grant Agency of the Czech Republic GAČR Award 16-16992S,
MŠMT ČR Grant LO1204, OTKA K135057, TKP 2021-NKTA-06, by RTI2018-093367-B-I00
and PID2021-122530OB-I00 from the Spanish State Research Agency (Ministry of Science andInnovation), co-ﬁnanced by the European Regional Development Fund (FEDER) from EU.

24

Plant Chromosome Biology: Cytogenetics meeting 2023

Session 1, Posters, September 11

9.
Towards an understanding of nuclear morphology andchromosome organization in endoreduplicated nuclei ofbarley seed tissues
Dr Anna Nowicka1, Mgr Luboslava Ferková1, Dr Mahmoud Said1, Mgr Martin Kovacik1,
Dr Jana Zwyrtková1, Dr Célia Baroux2, Assoc. prof. Ales Pecinka1
1. Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31,
779 00 Olomouc, Czech Republic
2. Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center,
University of Zürich, Zollikerstrasse 107, 8008 Zürich, Switzerland
Cereal grains represent a special type of seeds, with the largest part formed by theendosperm, a plant-unique tissue nourishing the developing and germinating embryo.
As a model in our study, we use barley, which has a large genome (2n = 2x = 14, 1C =4.8 Gbp) with interphase chromosomes organized in Rabl conﬁguration withcentromeres and telomeres positioned at the opposite nuclear poles. Using ﬂow-sorted
nuclei, we investigated nuclear morphology and chromosome organization in cycling
and endoreduplicated nuclei isolated from embryo and endosperm tissues ofdeveloping grains. We found that higher nuclear ploidy and developmental progression
alter the nuclear shape, cause nucleoli dispersion, generate a positional loss of sister
chromatid cohesion, and reduction in centromeric histone CENH3 abundance. This
coincided with the centromeres and telomeres dislocations within the nuclear space.
Interestingly, all nucleus- and chromatin changes were accompanied by reduced
genome stability, progressive loss of cell viability, and cell death. Altogether, this projectuncovers the complexity of nuclear and cellular processes during barley grain
development.

25

Plant Chromosome Biology: Cytogenetics meeting 2023

Session 1, Posters, September 11

10.
Effects of extensive chromosomal rearrangements in terms ofgenetics and epigenetics in Arabidopsis thaliana model plantOndřej Helia1, Barbora Matúšová2, Martin Lyčka1, Miloslava Fojtová1
1. Mendel Centre for Plant Genomics and Proteomics, Central European Institute ofTechnology (CEITEC), Masaryk University, 625 00 Brno, Czech Republic || National
Centre for Biomolecular Research, Faculty of Science, Masaryk University, 625 00
Brno, Czech Republic
2. National Centre for Biomolecular Research, Faculty of Science, Masaryk University,
625 00 Brno, Czech Republic
A demand for new crop varieties with maximum yield and resistance to biotic andabiotic stress conditions is accentuated by the global environmental changes of recent
years. Modern approaches of genetic engineering can contribute to obtaining thedesired traits. To this end, the CRISPR/Cas approach can be used. Importantly, it is evenpossible to simulate large-scale genome rearrangements mimicking those that occurred
naturally during plant evolution (Schindele et al., 2020). However, it is not yet known if
and how these genome changes will be reﬂected in subsequent generations of modiﬁed
plants. The focus of our research is the study of eﬀects of large-scale genome
modiﬁcations using homozygous lines of Arabidopsis thaliana with reciprocallytranslocated ends of long arms of chromosomes 1-2 and 1-5 (Beying et al., 2020). The
phenotypic diversity was observed in T4 generation of homozygous plants, in contrast
to T3 generation, where all translocated plants were comparable to the wild type line.
In addition to phenotype monitoring in subsequent generations, analyses of telomere
lengths, gene expression and chromatin structure are in progress. These analyses aresupposed to reveal whether and how chromatin organization is aﬀected in response tochanges in genome organization, and whether and how respective changes areinterrelated.
Funding: Czech Science Foundation, 22-04364S
References:
Schindele, A., Dorn, A., Puchta, H., 2020. CRISPR/Cas brings plant biology and breeding
into the fast lane. Current Opinion in Biotechnology 61, 7–14.
https://doi.org/10.1016/j.copbio.2019.08.006
Beying, N., Schmidt, C., Pacher, M., Houben, A., Puchta, H., 2020. CRISPR–Cas9mediated induction of heritable chromosomal translocations in Arabidopsis. Nature
Plants 6, 638–645. https://doi.org/10.1038/s41477-020-0663-x

26

Plant Chromosome Biology: Cytogenetics meeting 2023

Session 1, Posters, September 11

11.
Variability in mutual chromosome positioning in 3D space ofrice nuclei
Mgr. Alžběta Doležalová, Ph.D.1, Mgr. Denisa Beránková, Ph.D.1, Mgr. Eva Hřibová,
Ph.D.1
1. Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant
Structural and Functional Genomics, 77900 Olomouc, Czech Republic
Our study focuses on the 3D analysis of chromatin organization in rice (Oryza sativa,
2n = 2x = 24; 489 Mbp/1C). To assess the chromosome positioning in interphase nuclei,
chromosome oligo-painting was used to analyze their 3D distribution in G1 nuclei ofroot meristem and leave tissues. Six diﬀerent conﬁgurations of chromosome territories(CTs) were observed in the root G1 nuclei. In comparison, only four conﬁgurations wereobserved in leaf G1 nuclei. The volume of CTs and frequency of their association varied
also between the tissue types. CTs of chromosome 9 were usually separated (87 %) in
the root G1 meristematic nuclei. In leaf nuclei, CTs separation was less frequent (37 %).
Diﬀerences were observed also in the size of the nucleolus and the number and size of
45s rDNA loci. Finally, super-resolution microscopy (STED) revealed a more compact
and less relaxed structure of chromatin in diﬀerentiated G1 nuclei of leaves compared
to root meristem G1 nuclei. The average width of chromatin ﬁber in leaf G1 nuclei was
240 nm, compared to the root G1 where the width of the chromatin ﬁber was threetimes narrower (83 nm).

27

Plant Chromosome Biology: Cytogenetics meeting 2023

Session 1, Posters, September 11

12.
Chromosomal rearrangments and epigenetic consequences
Dr. Solmaz Khosravi1, Michelle Rönspies2, Rebecca Hinrichs2, Holger Puchta2, Andreas
Houben1
1. Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)
2. Botanical Institute, Karlsruhe Institute of Technology
There is a strong correlation between the epigenetic state of a DNA sequence and its
relative location on a chromosome. Compared to euchromatin referred as gene-richregions, heterochromatin referred as gene-poor regions show diﬀerent epigenetic
modiﬁcations including DNA methylation and histone modiﬁcations. To address thequestion whether the chromosomal position of a sequence has a critical inﬂuence on
the epigenetic state and activity of genes, CRISPR/Cas-based restructured Arabidopsis
thaliana chromosomes will be used.
Using CRISPR/Cas technology, chromosome rearrangements including translocation(rDNA repeats on Chromosome 2 and 4) and inversion (5 Mb pericentromeric region ofchromosome 3) events have been introduced. Subsequently, the Arabidopsis lines will
be used to decipher whether moving a sequence to a diﬀerent position on achromosome might change its epigenetic state and gene expression proﬁle.
To conﬁrm homozygous lines having translocation and inversion events, single-copyspeciﬁc FISH probes were designed which will be used on naturally extended
pachytene chromosomes. These lines will be used for ChIP-seq and whole genome
bisulﬁte sequencing to investigate whether changing the position of euchromatic andheterochromatic regions can inﬂuence the epigenetic patterns of the rearranged
regions at the sequence level.
In the next step, the Col0 lines (having inversion of a 5 Mb pericentromeric region on
chromosome 3) will be crossed with Ler-1 (having the same inversion) to observe if theepigenetic marks are inherited to the next generation. Considering that only the
euchromatic chromosome arms undergo genetic exchange as the basis of breeding
during meiosis, we will investigate whether the epigenetic state or chromosome
location is the main factor which aﬀects cross over. Using the F1 hybrids and SNP
analysis, we will evaluate whether the euchromatic region near the centromere or theheterochromatic region within a chromosomal arm are prone to cross overs, assumingthat the epigenetic state is conserved in both ecotypes. As a result, we ought to be able
to determine whether or not the epigenetic state is what suppresses cross overs.

28

Plant Chromosome Biology: Cytogenetics meeting 2023

Session 1, Posters, September 11

13.
Extensive chromosomal changes and seed geometricmorphometrics in Silene
Marcel Hubinský1, José Javier Martín Gómez2, Emilio Cervantes2, José Luis RodríguezLorenzo1
1

2

Plant Developmental Genetics, Institute of Biophysics v.v.i, Academy of Sciences of the
Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic

Instituto de Recursos Naturales y Agrobiología (Consejo Superior de Investigaciones
Cientíﬁcas), Cordel de Merinas 40, 37008 Salamanca, Spain

Plants may undergo diﬀerent natural changes, which dramatically modify their genomes. One
is polyploidization, which is the presence of more than two chromosome sets within a cell. The
second is hybridization, wich is the process of crossbreeding between genetically dissimilar
parents to produce a hybrid. Both are regarded as key factors for plant evolution and reﬂect
diﬀerences in fenotype in the diﬀerent plant organs. In Silene we can ﬁnd both examples innature, and this genus has a seed shape diversity long recognized as a valuable source of
information for infrageneric classiﬁcation. Morphometric analysis is the statistical study ofshape and size and their covariations with other variables. Shape is commonly described as theproperty of an object invariant under scaling, rotation, or translation. Traditionally, seed shapedescription was limited to an approximative comparison with geometric ﬁgures(rounded, globular, reniform or heart shape). Seed shape quantiﬁcation has been basedon direct measurements such as area, perimeter, length or width, narrowing statisticalanalysis. A geometrical approach involves mathematical equations. These equations
encompass morphological traits under complex genetic control. Looking at seed images,
or at their silhouettes, as geometric objects is a direct way to achieve mathematicalaccuracy in seed shape description. This is required for the combination of morphology
with genetics, ecology or taxonomy. We generated synthetic tetraploids of Silene
latifolia and performed controlled crosses between diploid S. latifolia and Silene dioica
as an approach to analyse seed morphology. After imaging capture and postprocessing,
we applied statistical analysis and we have found diﬀerences in the general seed shapeboth, in the tetraploids and in the hybrids. A detailed inspection through ﬂuorescencemicroscopy allowed the identiﬁcation of shape diﬀerences in the cells of the seed coat.
These diﬀerences, in the case of the hybrids, permitted us to identify what was the sexof both of the parents. Morphometry can be applied to any image processing including
cell microstructures, and provides mathematical accuracy for statistical analysis.

29Plant Chromosome Biology: Cytogenetics meeting 2023

Session 1, Posters, September 11

14.
Chromosomes at their ends – evolutionary perspectives
Eva Sykorova, Vratislav Peska, Petr Fajkus, Leon Jenner, Jiri Fajkus, Jana Fulneckova
Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
Mendel Centre for Plant Genomics and Proteomics, CEITEC Masaryk University, Brno, Czech
Republic

When organisms settled for linear chromosomes, the maintenance of their ends
became essential. Nucleoprotein complexes called telomeres were established to guard
chromosomal ends and genome stability. The telomerase-based mechanism looks likea winner for solving the problem of telomere DNA maintenance. Telomerase adds shorttandem repeats that were designated as typical telomere motifs in large groups for longtime, e.g. TTAGGG in vertebrates, TTTAGGG in plants. Our mapping of telomere
sequences across the eukaryotic tree of life led to identiﬁcation of novel telomere
repeats in various groups including algae, plants and animals, e.g. the unusual telomericrepeat CTCGGTTATGGG in onion. Phylogeny suggested that the telomere repeat
TTAGGG is an ancestral telomere type, but our results show that there is much moresequence variability, together with well-deﬁned switchpoints in telomere motif
evolution. Currently, a promising progress in plant telomerase research is made after
the plant RNA subunit in onion and other plants was discovered in 2019. Further
research identiﬁed plant TR subunits and deﬁned their evolutionary relationship in the
deep origin of plants and ciliates. Subsequently, further research led to theidentiﬁcation of TRs in Hymenoptera which share structural features similar to plant
TRs and distinct to vertebrate TRs. However, which features are critical for telomerefunction (repeat, mechanism, structure, proteins) will be discussed.
Research was supported by the Czech Science Foundation (project no. 20-01331X)

30

Plant Chromosome Biology: Cytogenetics meeting 2023

Session 1, Posters, September 11

15.
Nucleolar dominance in the allotetraploid model
grass Brachypodium hybridum – exploring molecularmechanisms behind the cytogenetic phenomenon.
Serhii Mykhailyk1, Natalia Borowska-Zuchowska1, Artur Piński1, Ales Kovarik2, Robert
Hasterok1
1. Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology
and Environmental Protection, Faculty of Natural Sciences, University of Silesia in
Katowice, Katowice, Poland
2. Department of Molecular Epigenetics, Institute of Biophysics, Czech Academy of
Sciences, Brno, Czech Republic
Nucleolar dominance (ND) is the epigenetic silencing of one set of ancestral 35S rRNA
genes (35S rDNA) in plant hybrids and allopolyploids. Despite being studied for
decades, the molecular mechanisms selecting a gene set predestined for repression
remain elusive. Brachypodium hybridum, an allotetraploid grass with a DDSS subgenome
composition (D subgenome derived from B. distachyon; S subgenome from B. stacei),
oﬀers a convenient model for investigating ND due to its relatively compact genome,
low content of repetitive sequences, and a single chromosomal pair carrying 35S rDNA
inherited from each progenitor. Moreover, the presence of diverse genotypes exhibiting
distinct 35S rDNA expression patterns, along with genetic resources and sequencing
data for multiple B. hybridum accessions and ancestral diploid species, strengthens its
suitability as a model to study ND.
Here, a population-level analysis of ND in B. hybridum was performed. The number andchromosomal distribution of 35S rDNA loci were determined by ﬂuorescence insitu hybridisation. The contributions of rDNA homoeologues in diﬀerent B.
hybridum genotypes were assessed by Southern hybridisation and bioinformatic
analysis of genomic Illumina reads. The expression of rDNA homoeologues at diﬀerent
developmental stages was analysed by RT-qPCR using locus-speciﬁc primers and RTCAPS. Finally, the methylation status of rRNA genes was determined in several B.
hybridum genotypes exhibiting diﬀerential expression of 35S rDNA. We conclude that
ND in B. hybridum is developmentally regulated in some but not all genotypes,
indicating population-speciﬁc regulation of ND.

31

Plant Chromosome Biology: Cytogenetics meeting 2023

September 11, 13:40-16:10

Session 2
Genome and chromosome evolution,
environmental response and plasticity
Talks

32

Plant Chromosome Biology: Cytogenetics meeting 2023

Session 2, Talk, 13:40-14:05

16.
The Crocus Chronicles: Decoding the Triploid Puzzle ofClonal Saffron Crocus
Abdullah El-nagish1,2, Ludwig Mann1, Seyedeh Sanam Kazemi Shahandashti3,4, Dörte
Harpke5, Zahra Nemati5, Maximilian W. Schmidt6, Susan Liedtke1, Frank R. Blattner5, Björn
Usadel3,4, Tony Heitkam1
1 Faculty of Biology, Institute of Botany, Technische Universität Dresden, Dresden, Germany
2 Botany and Microbiology Department, Faculty of Science, Sohag University, Sohag, Egypt
3 Institute of Biological Data Science, Heinrich-Heine Universität Düsseldorf, 40225 Düsseldorf,
Germany
4 IBG-4 Bioinformatics, Forschungszentrum Jülich, Wilhelm Johnen Str, 52428 Jülich, Germany
5 Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Gatersleben, Germany
6 Department of Grapevine Breeding, Hochschule of Geisenheim University
Saﬀron crocus (Crocus sativus L.), a sterile triploid (2n = 3x = 24), is a clonally propagated cropgrown for the production of saﬀron, the highest priced spice of the world. The evolutionary
origin of the triploid C. sativus was largely unknown and has been subject of debate since theearly 20th century. Recent cytogenetic and comparative next-generation sequencing
approaches pointed to ancient Greece as a point of origin for saﬀron and concluded that C.
sativus is an autotriploid species solely derived from heterogeneous cytotypes of C.
cartwrightianus (Schmidt et al. 2019, Nemati et al. 2019, reviewed in Kazemi-Shahandashti etal. 2022).
In our ongoing work, we target the processes before and after emergence of triploid saﬀron
crocus. With this, we can look into the past, present and future of this clonal line:(1) The past: How is chromosomal variability in the progenitor C. cartwrightianus? We detectedlarge diﬀerences in haplotype variability among chromosomes, suggesting that some C.
cartwrightianus chromosomes have obtained a higher genetic diversity across theMediterranean than others. This haplotype diversity is ﬁxed in saﬀron’s karyotype, a testimony
to the genetic variability of C. cartwrightianus 5000 years ago.
(2) The present: Are there signs of somaclonal variability in the saﬀron clone? By comparing
triploid saﬀron accessions across the globe, we detect chromosomal variability in three
independent instances. Based on the combinations of these three sites of chromosomal
variability, we conclude that at least four saﬀron lineages evolved somaclonally after emergenceof triploid saﬀron crocus. These saﬀron lineages have likely spread and are most probably
retained by vegetative propagation.
(3) The future: Can the global cultivation of the saﬀron crocus clone serve as a model for theepigenetics of adaptation? As the basis for comparative and epigenetic analyses, we areassembling reference genomes of the triploid saﬀron crocus and the diploid progenitor C.
cartwrightianus. We show the progress of sequencing, assembly and chromosomal anchoring.

33

Plant Chromosome Biology: Cytogenetics meeting 2023

Session 2, Talk, 14:05-14:25

17.
The impact of genome size on trait ﬂexibility, evolutionary
radiation and the distribution of angiosperms
Dr. Sreetama Bhadra1, Dr. Ilia J. Leitch2, Dr. Sidonie Bellot2, Dr. William J. Baker2,
Renske E. Onstein3
1. German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig,
Leipzig, Germany
2. Royal Botanic Gardens, Kew, UK
3. Naturalis Biodiversity Center, Leiden, The Netherland
Angiosperm diversity is a result of repeated evolutionary radiations. However, it isunclear how genomic factors contribute towards such radiations. Here, we test the
hypothesis that genome size acts as a potential driver of ‘trait ﬂexibility’ i.e., theevolvability of traits over macroevolutionary times, aﬀecting diversiﬁcation rates. We
integrate genome size, functional trait, distribution, and phylogenetic data for palms(Arecaceae)- a pantropical family comprising ca. 2,600 species – showing extraordinary
trait and genome size diversity. We used macroevolutionary and structural equation
models to show that palm lineages increased diversiﬁcation rates ca. 20 million years
ago, concordant with increased variation in genome sizes and traits. However, rates ofgenome size evolution were not associated with diversiﬁcation rates, but with fruit sizeand stem diameter evolutionary rates. Instead, fast diversiﬁcation rates were found forspecies with relatively large genomes, small fruits, and fast rates of stem height, fruit
length, or leaf size evolution. Our results provide evidence that genome size can act as
an inherent factor predisposing plants to trait ﬂexibility, and fast evolution of traits
provides the adaptability for lineages to persist and diversity. This may explain some of
the most enigmatic evolutionary radiations across angiosperms and their distribution
across the globe.

34

Plant Chromosome Biology: Cytogenetics meeting 2023

Session 2, Talk, 14:25-14:45

18.
Evolutionary Dynamics Of Tandem Repetitive Sequencesin Crepis sensu lato
dr hab Bozena Kolano1, dr Gülru Yücel2, dr Natalia Borowska-Zuchowska1, dr Maciej
Bisaga1, dr Magdalena Senderowicz1, dr Teresa Nowak1
1. Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
2. Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland;
Ondokuz Mayıs University, Agricultural Faculty, Samsun Türkiye;
Repetitive sequences are ubiquitous and fast-evolving elements responsible forgenome size variation and the large-scale organisation of plant genomes. Crepis
s.l. consists of primarily diploid species with relatively small numbers of large and welldiﬀerentiated chromosomes and high variation in genome size. This makes it a goodmodel system for investigating the organisation and diversiﬁcation of repetitiveelements. Bioinformatic, molecular and cytogenetic approaches were applied to study
the organisation and evolution of repetitive elements in some Crepis species.
Sequences were classiﬁed in terms of type and their abundance in the genome.
Comparative analyses of their genomic organisation and chromosomal distribution
were performed for groups of closely related species representing diﬀerent
evolutionary lineages of Crepis. Most identiﬁed repeats were speciﬁc to a small groupof closely related species. The comparative analyses of satellite repeats showed thatmost satellite families were characterised by species-speciﬁc chromosomal distribution
patterns. Usually, the overall patterns of the chromosomal distribution of an individual
satDNA were comparable in very closely related species with similar genome sizes. In
contrast, the more distantly related species, especially those whose speciation was
accompanied by extensive genome size changes, often showed distinct patterns of
satDNAs chromosomal distribution.
The study was ﬁnancially supported by the National Science Centre, Poland (ProjectNo. 2017/27/B/NZ8/01478) to BK and the Scientiﬁc and Technological ResearchCouncil of Türkiye (TÜBİTAK 2219 International Postdoctoral Research Fellowship
Program for Turkısh Cıtızens) to GY.

35

Plant Chromosome Biology: Cytogenetics meeting 2023

Session 2, Talk, 15:10-15:30

19.
Origin and evolution of diploid andallopolyploid Camelina genomes
Terezie Mandakova1, Perla Farhat1, Martin Lysak1
1. CEITEC Masaryk University
False ﬂax or gold of pleasure (Camelina sativa) is an increasingly popular oilseed crop
closely related to arabidopsis and canola. Despite the available sequenced genome andother genomic resources, the origin and putative parental genomes of theallohexaploid C. sativa (2n = 6x = 40) remained unknown. Nearly nothing was known
about the origin, genome evolution and phylogenetic relationships of diploid (2n = 12
and 14) and polyploid (2n = 26, 38, and 40) Camelina species. First, we established ﬁnescale comparative cytogenomic maps for all diploid, tetraploid andhexaploid Camelina species and elucidated the origin of polyploid genome andphylogenetic relationships between Camelina species. We identiﬁed parental genomesof the known allopolyploid species (C. intermedia, C. microcarpa, C. rumelica and C.
sativa) and reconstructed the sequence of hybridization events. Besides common
structural rearrangements, such as translocations and inversions, complex dysploidal
chromosomal rearrangements generated shattered chromosomes in Camelina diploids.
The nature of these rearrangements was further analyzed using chromosome-level
genome assemblies of four diploid Camelina genomes. These complex chromosomal
alterations, similar to chromoplexies associated with several human disorders, have notbeen reported in a non-model diploid plant species as yet.
This study was supported by a research grant from the Czech Science Foundation (grantno. 21-03909S).

36

Plant Chromosome Biology: Cytogenetics meeting 2023

Session 2, Talk, 15:50-16:10

20.
Prospero’s magic: when karyotypic and genomic changes
drive diversiﬁcation (and the phenotype does not keep up)
Dr. Hanna Weiss-Schneeweiss1, Dr. Tae-Soo Jang2, Dr. John Parker3
1. University of Vienna, Department of Botany and Biodiversity Research, Rennweg
14, A-1030 Vienna, Austria
2. Department of Biology, College of Bioscience and Biotechnology, Chungnam
National University, Daejeon 34134, Korea
3. Cambridge University Botanic Garden, Cambridge, CB2 1JF, UK
The Prospero autumnale complex (Hyacinthaceae) is chromosomally remarkably
variable. Phylogenetic and genomic analyses of hundreds of individually karyotyped
plants from the entire distribution range of the complex revealed that the observed
variation is very structured, both geographically and karyotypically. Three major
processes creating these intricate and complex patterns of variation were identiﬁed: (1)dysploidy on diploid level (chromosome base numbers of x = 5, 6, 7 or 8) likely with lowlevels of karyotype restructuring, (2) recurrent auto- and allopolyploidizationaccompanied by backcrossing to the parental diploid(s) and/or inter-polyploid crossing,and (3) genome size dynamics due to proportional changes in dispersed repeat lineages
and non-proportional changes in tandem repeat families, exclusively found and/or
uniquely ampliﬁed in individual cytotypes. Yet another level of complexity stems fromyoung and recurrently formed B-chromosomes and evolutionarily older euchromatic
supernumerary chromosomal segments (SCSs). This enormous karyotypic variation is,
however, not paralleled by phenotypic diversiﬁcation as morphometric analyses failed
to identify any character combinations for unambiguous cytotype identiﬁcation. The
karyotypic variation is not only tolerated, but emerges as a main driver of the evolutionof this species complex, which, rather uniquely for bulbous species, propagates only
sexually.

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Plant Chromosome Biology: Cytogenetics meeting 2023

Session 2, Talk, 15:50-16:10

21.
Insights into chromosome and repetitive sequence evolution
in Musaceae from long-molecule, t2t genome assemblies
and molecular cytogenetics
Dr Trude Schwarzacher1, Dr Ziwei Wang2, Ms Dongli Cui3, Dr Mathieu Rouard4, ProfPat (J.S.) Heslop-Harrison1, Qing Liu3
1. University of Leicester, Department of Genetics and Genome Biology, Institute forEnvironmental Futures and Key Laboratory of Plant Resources Conservation andSustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany,
South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
2. Henry Fok School of Biology and Agriculture, Shaoguan University, Shaoguan, China
3. Key Laboratory of Plant Resources Conservation and Sustainable Utilization /Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical
Garden, Chinese Academy of Sciences, Guangzhou, China
4. Bioversity International, Parc Scientiﬁque Agropolis II, Montpellier, France
The family Musaceae, with three genera Musa, Musella and Ensete, includes important
crops and ornamental species. To understand their genome evolution, we combined
data from chromosome scale assemblies with ﬂuorescent in situ hybridization todescribe the chromosomal rearrangements and repetitive DNA composition. Some 5060% of the genomes are composed of repetitive sequences with LTR-retroelements
and DNA transposons predominant and their families distributed among diﬀerent
groups of species. A tandemly repeated 134bp satellite sequence is present at thecentromeres of Ensete glaucum, E. ventricosum and Musella lasiocarpa, but no tandem
repeat is in Musa centromeres. 45S rDNA and 5S rDNA have variable numbers andchromosomal locations and occupy often otherwise non-syntenic arms. Thus, rDNA
sites seem to move independently and associate with diﬀerent chromosomal
environments; the arm carrying 45S rDNA in E. glaucum is depleted in genes, but thearms with 45S rDNA in M. lasiocarpa have a similar gene density to other chromosome
arms. The telomere-to-telomere assemblies, including centromeric positions, enabled
us to characterize the chromosomal rearrangements. Musella and Ensete, both x=9,
show only few whole arm translocations and large regions of synteny supporting theclose relationship but separation of genera, while the x=11 Musa species are
phylogenetically separate with many more postulated chromosomal rearrangements
and genetic diﬀerences. This insights into the chromosomal and repetitive sequence
evolution of Musaceae along with gene sequences in the assemblies, add to acomprehensive and robust pangenome of Musa and Ensete, valuable to understanding
evolutionary mechanisms and for crop improvement.

38

Plant Chromosome Biology: Cytogenetics meeting 2023

Session 2, Posters, September 11

Session 2
Genome and chromosome evolution,
environmental response and plasticity
Posters39

Plant Chromosome Biology: Cytogenetics meeting 2023

Session 2, Posters, September 11

22.
Dysploidy in spring crocuses (Crocus series Verni)
Nomar Waminal1, Frank Blattner1, Dörte Harpke1
1. Leibniz Institute of Plant Genetics and Crop Plant Research (IPK-Gatersleben)
Spring crocuses, which comprise ten diploid and two polyploid species, as well as apolyploid complex, show diverse chromosome numbers (2n = 8, 10, 12, 14, 16, 18, 20,
22, 28), indicating dysploid karyotype changes. Thus, this taxon provides theopportunity to analyze mechanisms driving fast karyotype evolution. Here, we gather
insights into dysploidy in Crocus ser. Verni by analyzing the genomic dynamics ofrepetitive elements. We characterized the types and abundances of repetitive genomic
elements from each taxon and performed a comparative karyotype analysis in aphylogenomic context. Crocus longiﬂorus, which has 2n = 28 chromosomes, has thesmallest genome size (2C = 3.2 pg), whereas taxa with fewer chromosomes haveincreased genome sizes. Repeat quantiﬁcation and FISH analysis of six repeat probes
suggest a concerted action of descending dysploidy and a burst of transposable
elements (Ty1/Copia and Ty3/Gypsy) as drivers to the reduction of chromosome
number while increasing genome size in more recently evolved taxa. This work provides
insights into dysploidy in ser. Verni and an opportunity to develop approaches to study
other dysploid-rich clades in plants.

40

Plant Chromosome Biology: Cytogenetics meeting 2023

Session 2, Posters, September 11

23.
The pathways of whole-genome duplications, diploidization,and descending dysploidy in the Biscutelleae (Brassicaceae)
Yile Huang1, Hussein Anani1, Terezie Mandáková1, Xinyi Guo1, Manuel Poretti2,
Christian Parisod2, Martin Lysak1
1. Central European Institute of Technology (CEITEC), Masaryk University
2. Department of Biology, University of Fribourg
In plants, whole-genome duplications (WGDs) are often characterized by genome-wide
diploidization including descending dysploidy, i.e., chromosomal rearrangements that
reduce chromosome number and genome size. However, the genomic basis andevolutionary signiﬁcance of chromosomal restructuring remain poorly understood.
Phylogenetic and comparative genomic analyses revealed that the Biscutelleae consistof one diploid (Megadenia), one neotetraploid (Heldreichia), and three mesotetraploid(Biscutella, Lunaria, and Ricotia) genera, with the ancestral tetraploid genomes arisingfrom independent WGD events involving closely related diploid genomes. Here, wesequenced, analyzed and compared genomes of four Biscutella species (Buckler
Mustards) diﬀering by genome sizes (0.7 to 1.1 Gbp) and chromosome numbers (n = 6
and 8). Genome sequence data with long-range scaﬀolding combined with molecular
cytogenetics provided accurate assemblies and annotations at the chromosome level.
Highly reshuﬄed Biscutella genomes have descended from two ancPCK-like ancestralgenomes via allopolyploidy followed by extensive descending dysploidy (n = 16 → n =6 and 8). Such genome restructuring mediating descending dysploidies and speciation
appeared to be predominantly non-random, with large chromosomal segments
conserved as duplicates, while others exhibited considerable turnover. Our results
provide new insights into the role of dysploid changes in plant genome evolution,
speciation, and diversiﬁcation. Czech Science Foundation, project 21-07748L.

41

Plant Chromosome Biology: Cytogenetics meeting 2023

Session 2, Posters, September 11

24.
Urban environments, chromosome formula andpolyploidization in two Commelina species
Hina Shimomai1, Taichi Nakata1, Dr. Koki Katsuhara2, Dr. Seiji Kato1, Prof. Atsushi
Ushimaru1, Prof. Nobuko Ohmido1
1. Graduate School of Human Development and Environment, Kobe University
2. Okayama University
Urbanization largely changes biodiversity and natural environments. Few studies haveinvestigated plant adaptation to urban environments based on both ecological andmolecular cytological approaches. We focus on two annual plants, Commelina
communis (Cc) and its related species, C.cfciliata (Ccf) which grow widely in Asia and arehighly diverse both in morphological traits and chromosome numbers (Ccf; 2n=46 andCc; 2n=88). We demonstrate how plants adapt to urban environments by investigating
the distribution in urban-rural gradients, the comparison of stomata and genome size,and chromosome karyotyping. As a result, Cc was distributed widely from rural to urban
areas, while Ccf were found only in rural areas. The stomata length of Cc wassigniﬁcantly longer, and Cc had double genome size, compared to that of Ccf. Ccf
chromosomes were detected on a part of Cc chromosomes by GISH. From these results,
the large stomata size of Cc seems due to polyploidy, and polyploidy might give Cc tohave a high potential to adapt to urban environments compared to Ccf. This is the ﬁrst
investigation to clarify the distribution diﬀerence relating to urbanization, thediﬀerence in stomata and genome size, and to conduct chromosome karyotyping in
two Commelina species. However, there was no signiﬁcant relationship between
stomata size and urbanization in the regional comparisons. In this presentation, we
discuss the mechanism of plant adaptation in urban environments focusing on therelationship between the eﬀects of human activity and genetic traits which leads to theecological diﬀerence in nature plants.

42

Plant Chromosome Biology: Cytogenetics meeting 2023

Session 2, Posters, September 1125.
Major genotype-panels for Hydrangea genomics bycomparative repeat analysis
Sara Ishiguro1, Dr. Nicola Schmidt2, Prof. Dr. Nobuko Ohmido1
1. Kobe University
2. Technische Universität Dresden
Hydrangea is a popular garden plant due to its ornamental value. However, hybridization
has been performed primarily based on its morphological traits, resulting in unknown
genetic diversity, species origin, and phylogeny. Analysis of repetitive elements
in Hydrangea species is a key for understanding its genetic diversities and achievementsof genetic resources for elaborate breeding. In this study, whole genome sequencing(WGS) and comparative graph-based-clustering analyses were performed using Repeat
Explorer pipeline to characterize and compare repetitive elements within
representative six Hydrangea species with diﬀerent origins and chromosome numbers.
The LTR retrotransposons are the most abundant repetitive elements within
the Hydrangea genomes. Comparative clustering analysis divided into four groups
based on the composition and abundance of identiﬁed repeats in their genomes;
Japanese
diploid Hydrangea species
(GAK,
TAM,
and
EZO),
Japanese
polyploid Hydrangea (NOR), Chinese Hydrangea (STR), and American Hydrangea (ANN).
Tekay elements in H. paniculata (NOR) genome are independently developed fromJapanese diploid species whereas Ale elements are conserved between NOR andJapanese diploid species. Thus, we demonstrate that NOR is polyploidized anddiﬀerentiated independently from ancient Japanese diploid species, followed by sharing
the abundance and composition of Ale elements by the horizontal transmission. In
addition, satellite DNAs (satDNAs) landscape of NOR genome suggests that NOR
genome has two genetic genealogies from Japanese diploid Hydrangea andChinese Hydrangea species. In this presentation, we will also discuss the results oflocalize those repetitive satDNAs on Hydrangea chromosomes by FISH.

43

Plant Chromosome Biology: Cytogenetics meeting 2023

Session 2, Posters, September 11

26.
The ampliﬁcation of interstitial telomeric repeats
accompanied genome evolution in the East Asian
genus Yinshania (Brassicaceae)
Xinyi Guo1, Hongliang Chen2, Terezie Mandáková1, Pavel Trávníček3, Yingxiong Qiu2,
Hang Sun4, Martin Lysák1
1. Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech
Republic
2. Laboratory of Systematics & Evolutionary Botany and Biodiversity, College of Life
Science, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China
3. Institute of Botany of the Czech Academy of Sciences, Průhonice, Czech Republic
4. CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming
Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, P. R.
China
Hybridization plays a key role in genomic divergence and speciation in plants. However,
little is known about the variation in karyotypes and repetitive sequences during
genome evolution enabled by hybridization. Here, we present an integrative
cytogenomic study of the small crucifer genus Yinshania (c. six species), endemic tonorthern and southwestern China. Two infrageneric clades were identiﬁed andhybridization was detected both within and between clades. While three species (Y.
acutangula, Y. exiensis, and Y. wilsonii) are diploid (2n = 12) and two (Y. microcarpa and Y.
zayuensis) are tetraploid (2n = 24), Y. henryi includes both cytotypes. The diploid
genomes have the same structure, which probably originated from an ancestral genome
with eight chromosomes by descending dysploidy via two end-to-end translocations.
The genomes of Y. microcarpa and Y. zayuensis are allotetraploid, whereas the tetraploid
genome of Y. henryi is most likely an autotetraploid. The chromosome-scale genome
assembly of Y. wilsonii corroborated the structure of the diploid karyotype and revealed
slow genic evolution with distinct dynamics of major retrotransposon clades. In
addition, we observed high variation in the number of 35 rDNA and tandem repeat lociamong species. Interestingly, TTTAGGG-type telomeric repeats and their variants wereidentiﬁed as the most abundant satellite family in all Yinshania genomes. The
presence/absence of the TTTAGCG variant appears to be associated with infragenericcladogenesis. These simple tandem repeats were frequently associated with CRM
retrotransposons and together form large loci at pericentromeres of all chromosomes.
This work was supported by a research grant from the Czech Science Foundation (2003419Y).

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Plant Chromosome Biology: Cytogenetics meeting 2023

Session 2, Posters, September 11

27.
Does the time matter? Revealing the pathways of rRNA gene
evolutionin Brachypodium hybridum of different evolutionaryage.
Dana Trunova1, Natalia Borowska-Zuchowska1, Serhii Mykhailyk1, Kai Xia2, YuanBin
Zhu2, Rubén Sancho3, Pilar Catalan3, Ales Kovarik4, Kai Wang2, Robert Hasterok1,
Bozena Kolano1
1. Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural
Sciences, University of Silesia in Katowice, Katowice 40-032, Poland
2. School of Life Sciences, Nantong University, Nantong 226019, Jiangsu, China
3. Department of Agricultural and Environmental Sciences, High Polytechnic School of
Huesca, University of Zaragoza, Huesca 22071, Spain; Grupo de Bioquímica,
Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC,
Zaragoza E-50059, Spain
4. Department of Molecular Epigenetics, Institute of Biophysics, Czech Academy of
Sciences, CZ-61200 Brno, Czech Republic
Ribosomal RNA genes (rDNA) encode the essential components of ribosomes, which
are the cellular machinery responsible for protein synthesis. These genes consist ofconserved genic and variable non-coding regions, providing a valuable tool for studying
phylogenetic relationships and genome evolution. Previous studies of the rRNA genes
in Brachypodium hybridum (a model allotetraploid grass originating from the diploidevolutionary ancestors similar to contemporary B. distachyon and B. stacei) mainly
focused on the 35S rDNA. It has been shown that interaction between the ancestralgenomes results in nuclear dominance and reduction of the copy number against oneof the parental variants of 35S rDNA in numerous accessions of B. hybridum. In contrast,
little is known about the organization of 5S rDNA in B. hybridum. In this study, we
focused on two lineages of B. hybridum with diﬀerent ages (0.14 Ma and 1.4 Ma) oforigin. The 5S and 35S rRNA gene organization analyses have been performed using
molecular (Southern Blot, gCAPS), cytogenetic (FISH) and bioinformatic approaches.
The chromosomal distribution of 5S and 35S rDNA showed the uniparental loss of lociin B. hybridum Bhyb26, representing an ancient lineage. Furthermore, evidence of
homogenization of rDNA was found. Our results shed more light on the evolutionary
pathways of rDNA structure and evolution in this important model grass.
The research was funded by the National Science Centre, Poland (project
number2020/39/O/NZ8/00184) to BK and DT.

45

Plant Chromosome Biology: Cytogenetics meeting 2023

Session 2, Posters, September 11

29.
Evolution of the family Musaceae through large chromosomal
rearrangements
Jana Čížková1, Denisa Beránková1, Simona Martikánová1, Eva Hřibová1
1. Centre of Plant Structural and Functional Genomics, Institute of Experimental
BotanyThe evolution of the family Musaceae was accompanied by whole genome duplication
followed by diploidization and fractionation of the genome. Large-scale chromosomal
rearrangements played a key role in diversiﬁcation and speciation. The
family Musaceae comprises genera Musa, Ensete and Musella. While Ensete (2n=18)
and Musella (2n=18) are represented by few species, genus Musa contains about 70
diﬀerent species, which are classiﬁed into four sections. The largest of them, Eumusa(x=11), comprises most of edible banana cultivars. Closely related section
Rhodochlamys (x=11) contains ornamental species. Section Australimusa (x=10)
contains a peculiar group of edible banana clones known as Fe‘i. The last section,
Callimusa (x=9, 10), is the most diverse one and includes species closely related
to Ensete and Musella.
With the aim to identify and compare structural chromosome changes and to
shed light on karyotype evolution in Musaceae, we used oligo painting FISH. We
observed numerous chromosomal rearrangements, some of which were shared inclosely related species. Translocation breakpoints were identiﬁed in assembled Oxford
Nanopore data by a newly developed bioinformatic pipeline. Together withphylogenetic analysis and divergence time estimation of the main clades and selected
species of Musaceae, we suggested the most probable mode of karyotype evolution.

46

Plant Chromosome Biology: Cytogenetics meeting 2023

Session 2, Posters, September 1130.
Nucleotide level structure of 5S rDNA loci in the great
duckweed, Spirodela polyrhiza
Dr Anton Stepanenko1,6, Ms Guimin Chen2, Dr Phuong T. N. Hoang3, Prof Todd
Michael4, Prof Eric Lam5, Prof Ingo Schubert6, Prof Nikolai Borisjuk2
1. Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake andJiangsu Collaborative Innovation, School of Life Sciences Huaiyin Normal University,
Huai’an, China;
2. Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake andJiangsu Collaborative Innovation, School of Life Sciences Huaiyin Normal University,
Huai’an, China;
3. Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben,
Germany; Faculty of Biology, Dalat University, Ðà Lat, Vietnam
4. The Plant Molecular and Cellular Biology Laboratory, The Salk Institute for
Biological Studies, La Jolla, USA
5. Department of Plant Biology and Pathology, Rutgers, the State University of New
Jersey, New Brunswick, USA
6. Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben,
Germany
7. Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake andJiangsu Collaborative Innovation, School of Life Sciences Huaiyin Normal University,
Huai’an, China
The ribosomal DNA (rDNA) plays an important part in eukaryotes by encoding four ribosomal
RNAs necessary for ribosome biogenesis, thus regulating organism’s growth and development.
Although intensively characterized cytogenetically in many plant taxa, the 5S and 35S rDNA
loci are usually excluded from description of whole genome sequences because of their
redundancy in hundreds to thousands tandemly arranged copies. Taking advantage of theuniquely low rDNA copy number in the monocot aquatic plant great duckweed, Spirodela
polyrhiza (Lemnaceae), we revealed the detailed molecular organization of the 5S rDNA locicombining molecular cytology, conventional and extra-long Oxford Nanopore (ON) sequencing.
While in situ hybridization detected a single 5S rDNA locus on S. polyrhiza chromosomes, theON reads revealed two clusters of 5S rDNA units, one containing 60 copies of tandemly
repeated units of about 1100 bp and a second cluster with 40 copies of ~500 bp repeated units.
Both clusters are surrounded by highly AT-enriched sequences mapped correspondingly to S.
polyrhiza chromosomes 13 and 6. The ON sequencing gave a reliable estimate of the 5S rDNA
unit copy number, which was conﬁrmed by quantitative PCR, however gene sequences were
untypically heterogeneous compared to usually highly homogenized plant rDNA repeats.
Validation of the rough ON data by sequencing multiple plasmids containing PCR fragments
covering individual 5S rDNA units demonstrated that both clusters contained the conservative
119bp long sequence encoding 5S rDNA followed by the locus-speciﬁc intergenic spacer (IGS).
In the locus of ChrS13, the 5S rRNA coding sequences were spaced by IGSs of 1056-1069 bp,
and by the IGS of 400bp in the locus of ChrS6. To the best of our knowledge, the obtained dataon 5S rRNA in Spirodela polyrhiza, makes the rDNA loci of this species most completely
characterized among the ﬂowering plants.

47

Plant Chromosome Biology: Cytogenetics meeting 2023

Session 2, Posters, September 11

31.
Evolving together: Cassandra retrotransposons gradually
mirror promoter mutations of the 5S rRNA genes
Sophie Maiwald1, Ludwig Mann1, Dr. Sònia Garcia2, Dr. Tony Heitkam1
1. Faculty of Biology, TU Dresden
2. Institut Botànic de Barcelona
The 5S rRNA genes are among the most conserved nucleotide sequences across all
species. Similar to the 5S preservation we observe the occurrence of 5S-related nonautonomous retrotransposons, so-called Cassandra. Cassandras harbor highly
conserved 5S rDNA-related sequences within their long terminal repeats (LTRs),
advantageously providing them with the 5S internal promoter. However, the dynamics
of Cassandra retrotransposon evolution in the context of 5S rRNA gene sequence
information and structural arrangement are still unclear, especially: 1) do we observe
repeated or gradual domestication of the highly conserved 5S promoter by Cassandras
and 2) do changes in 5S organization such as in the linked 35S-5S rDNA arrangements
impact Cassandra evolution? Here, we show evidence for gradual co-evolution of
Cassandra sequences with their corresponding 5S rDNAs. To follow the impact of 5S
rDNA variability on Cassandra TEs, we investigate the Asteraceae family where highlyvariable 5S rDNAs, including 5S promoter shifts and both linked and separated 35S-5S
rDNA arrangements have been reported. Cassandras within the Asteraceae mirror 5S
rDNA promoter mutations of their host genome, likely as an adaptation to the host’s
speciﬁc 5S transcription factors and hence compensating for evolutionary changes in
the 5S rDNA sequence. Changes in the 5S rDNA sequence and in Cassandras seem
uncorrelated with linked/separated rDNA arrangements. We place all theseobservations into the context of angiosperm 5S rDNA-Cassandra evolution, discuss
Cassandra’s origin hypotheses (single or multiple) and Cassandra’s possible impact on
rDNA and plant genome organization, giving new insights into the interplay ofribosomal genes and transposable elements.

48

Plant Chromosome Biology: Cytogenetics meeting 2023

Session 2, Posters, September 11

32.
Polyploidy-driven genome evolution of the South African
genus Heliophila (Brassicaceae)
Milan Pouch1, Petr Šmarda2, Yile Huang1, Pieter Winter3, Ihsan A. Al-Shehbaz4, Martin
A. Lysak1, Terezie Mandáková5
1. CEITEC – Central European Institute of Technology, Masaryk University, Brno,
Czech Republic and National Centre for Biomolecular Research, Faculty of Science,
Masaryk University, Brno, Czech Republic
2. Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno,
Czech Republic
3. South African National Biodiversity Institute (SANBI), Kirstenbosch, Cape Town,
South Africa
4. Missouri Botanical Garden, St. Louis, MO, United States
5. CEITEC – Central European Institute of Technology, Masaryk University, Brno,
Czech Republic and Institute of Experimental Biology, Faculty of Science, Masaryk
University, Brno, Czech Republic
The tribe Heliophileae in the family Brassicaceae displays remarkable morphologicaldiversity, that distinguishes it from other crucifer tribes. Endemic to southern Africa,
this tribe thrives in biodiversity hotspots where polyploidy is traditionally not
associated with diversiﬁcation and speciation events. Our comprehensive study
integrates molecular phylogenetics, genomics, cytogenetics, ecology, and taxonomy toinvestigate Heliophileae, encompassing about 70 Heliophila species with varying
chromosome numbers (2n = 16 - 80). A large-scale phylogenetic analysis of more than
400 accessions revealed four major infrageneric clades that diversiﬁed between 12 to
ﬁvemillion
years
ago.
Using
chromosome-scale
genomeassemblyof Heliophila variabilis (n = 11, 334 Mb), we discovered two pairs of diﬀerentiallyfractionated subgenomes, indicating an allo-octoploid origin of the genome andHeliophileae. The putative octoploid ancestral genome (2n = 8x = 60) likely emerged
from hybridization between two distinct allotetraploids (2n = 4x = 30), followed bypost-polyploid diploidization and clade-/species-speciﬁc descending dysploidies (30 →16 - 26). Here, we examine chromosome number evolution during diploidization among
and within major Heliophila clades in South Africa and test the extent to which
infrageneric cladogenesis and genome diploidization follow geographic, edaphic and(paleo)climatic patterns as well as ecological life histories.

49

Plant Chromosome Biology: Cytogenetics meeting 2023

Session 2, Posters, September 11

33.
Independent and recurrent dysploidy eventsin Phaseolus beans
Thiago Nascimento1, André Marques2, Andrea Pedrosa-Harand1
1. Federal University of Pernambuco
2. Max-Planck Institute for Plant Breeding Research
Beans from Phaseolus genus are well known for their importance as a protein source forhumans, specially provided by cultivated species as the common bean and lima bean.
Most Phaseolus species have a conserved karyotype number with 2n = 22, except for
the Leptostachyus group, a ~1.3 My clade comprising three species with 2n = 20. Its
ancestral underwent a descending dysploidy event promoted by a nested chromosome
fusion. In this work, we investigated the karyotype evolution of Phaseolus species fromthe Filiformis group, using oligo-FISH painting probes for chromosomes 1, 2, 3 and 5,
plus 5S and 35S rDNA. Our data revealed the existence of a new dysploid species
outside of the Leptostachyus group, P. angustissimus (Filiformis group; ~2,9 My), alsowith 20 chromosomes; however, other species of this group showed 2n = 22. Phaseolus
angustissimus also underwent genome reshuﬄing, although with less structural
rearrangements then P. leptostachyus. Our new ﬁndings revealed that dysploidy eventsin Phaseolus are recurrent, despite the absence of a previous whole genome
duplication; and points to the necessity of further investigations for elucidating
chromosome evolution in beans.

50Plant Chromosome Biology: Cytogenetics meeting 2023

Session 2, Posters, September 11

34.
Repeat turnover meets stable chromosomes: Repetitive
DNAs mark speciation and gene pool boundaries in sugar
beet and wild beets
Nicola Schmidt1, Katharina Sielemann2, Sarah Breitenbach1, Jörg Fuchs3, Boas Pucker4,
Bernd Weisshaar2, Daniela Holtgräwe2, Tony Heitkam1
1. TU Dresden
2. Bielefeld University
3. IPK Gatersleben
4. TU Braunschweig
Sugar beet (Beta vulgaris) and all wild beet relatives share a base chromosome number of nineand similar chromosome morphologies. Yet, interspeciﬁc breeding is impeded by chromosome
and sequence divergence that is still not fully understood. As repetitive DNAs are the fastest
evolving parts of the genome, they likely impact genomic variability and contribute to theseparation of the beet gene pools. Hence, we ask if innovations and losses in the repeatome
can be linked to chromosomal diﬀerentiation and speciation.
We traced genome and chromosome-wide evolution across sugar beet and twelve wild beets
comprising all sections of the beet genera Beta and Patellifolia. For this, we combined short andlong read sequencing, ﬂow cytometry, bioinformatics and cytogenetics to build acomprehensive framework for our beet panel that spans the complete scale from DNA tochromosome to genome. Both, genome sizes (694 Mbp in the diploid B.
vulgaris subsp. maritima to 2,471 Mbp in the pentaploid B. intermedia) and repeat proﬁles (5368% repeats), reﬂect the separation of the beets into gene pools in such a way that speciﬁc
repeats show contrasting evolutionary patterns: We identiﬁed the section- and species-speciﬁc
repeat emergences and losses, e.g. of the retrotransposons causal for genome expansions inthe section Corollinae/Nanae. As most genomic variability lies in the satellite DNAs, we thenfocus on tracing the 19 beetSat families across the three beet sections/genera. These taxa
harbor evidence for contrasting strategies in repeat evolution, leading to contrasting satellite
DNA proﬁles and fundamentally diﬀerent centromere architectures, ranging from chromosomal
uniformity in Beta and Patellifolia species and the formation of patchwork chromosomesin Corollinae/Nanae species.
We show that repetitive DNAs are causal for the genome expansions and contractions acrossthe beet genera, providing insights into the genomic underpinnings of beet speciation. Satellite
DNAs in particular vary considerably between beet genomes, leading to the evolution of
distinct chromosomal setups in the three gene pools, likely contributing to the barriers in beetbreeding. Thus, with their isokaryotypic chromosome sets, beet genomes present an ideal
system for studying the link between repeats, genomic variability, and chromosomal
diﬀerentiation and provide a theoretical fundament for understanding barriers in any crop
breeding eﬀort.

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Plant Chromosome Biology: Cytogenetics meeting 2023

September 11, 16:55-18:40

Session 3
New tools, perspectives and applications
Talks

52

Plant Chromosome Biology: Cytogenetics meeting 2023

Session 3, Talk, 16:55-17:20

35.
Let them move: ﬂow cytometric chromosome analysis
and sorting
Jaroslav Doležel1
1. Institute of Experimental Botany of the Czech Academy of Sciences, Centre of
Plant Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc,Czech Republic
Condensed mitotic chromosomes have traditionally been studied using microscopy
after they are immobilized on a ﬂat surface. However, it is also possible to analyze themduring movement in a narrow stream of liquid using ﬂow cytometry. The so-called ﬂow
karyotyping, classiﬁes chromosomes according to relative DNA content and/or theamount of particular DNA repeats. As the results are less informative compared tothose obtained using molecular cytogenetics, ﬂow karyotyping has been useful only inparticular cases. The real power of ﬂow cytometric chromosome analysis lies in theability to purify mitotic chromosomes by sorting either in bulk, or just a particularchromosome for downstream analysis. Importantly, the morphology of ﬂow-sorted
chromosomes is well preserved, their DNA is intact and suitable for a range ofapplications. Dissecting genomes to individual chromosomes greatly simpliﬁed gene
mapping and cloning as well as assembling sequences of complex genomes. The ability
to purify mitotic metaphase chromosomes made it possible to describe threedimensional organization of DNA and characterize their protein composition. The
examination of puriﬁed chromosomes using environmental scanning electron
microscopy revealed a unique organization of perichromosomal layer. The analysis andsorting using ﬂow cytometry thus ideally complements microscopic observations andfacilitates the study of nuclear genomes and their building blocks – chromosomes.
Keywords: 3D chromatin organization, Chromosome proteome, Chromosome
ultrastructure, Genome sequencing, Gene cloning, Perichromosomal layer

53

Plant Chromosome Biology: Cytogenetics meeting 2023

Session 3, Talk, 17:20-17:40

36.
A 3C view of 3D genome dynamics in barley
Hana Šimková1, Petr Cápal1, Amanda Souza Camara2, Pavla Navrátilová1, Alžběta
Doležalová1, Jaroslav Doležel1, Martin Mascher2
1. Institute of Experimental Botany, Czech Academy of Sciences
2. Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)
Chromosomes undergo marked structural metamorphoses during the cell cycle. During
interphase, relaxed chromatin is stored in the cell nucleus, being folded at several levels.
Its ﬂexible arrangement must ensure that the correct gene expression programs are
executed at the right time and in the right cell type and that the chromatin can be
rapidly reorganized into highly condensed structures – metaphase chromosomes, which
are essential for a safe transfer of genetic information into the next generation.
Mechanics of these processes is underexplored in plants. Emergence of novel moleculartechniques based on chromatin conformation capture, Hi-C in particular, enable
studying the 3D chromatin dynamics on the DNA level.
Taking barley as a model, we coupled Hi-C with ﬂow sorting, which enabled puriﬁcationof metaphase chromosomes and nuclei at G1, S and G2 phase, respectively. Polymer
modelling based on Hi-C data from the metaphase chromosomes suggested helicalfolding of the DNA with ~30 Mb per turn. Analysis of Hi-C data from G1, S and G2
revealed relatively small changes in chromatin condensation in nuclei from root tips but
a striking diﬀerence between root-tip G1 and G0/G1 of a leaf tissue, suggesting distinct
interphase chromatin arrangement between rapidly cycling and non-cycling cells. Ourdata, supported by microscopy observations, point to several diﬀerences in higherorder chromatin organisation between plants and animals.

54

Plant Chromosome Biology: Cytogenetics meeting 2023

Session 3, Talk, 17:40-18:00

37.
RepeatExplorer tools for genome annotations
Petr Novák1, Pavel Neumann1, Nina Hoštáková1, Jiří Macas1
1. Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology,České Budějovice, Czechia
The RepeatExplorer Galaxy web server, originally designed to annotate repeats in genomes
where assembly was not available, has grown in tandem with advancements in sequencing
technologies. As high-quality genome assemblies have become routinely available, the server
has incorporated novel tools for annotating repeats in these assemblies. The new tools,
including DANTE, DANTE-LTR, and TideCluster, combine assembly-free approaches, similaritybased annotation, and feature-based annotation.
DANTE (Domain-based ANnotation of Transposable Elements) utilizes the REXdb database ofconserved domains to detect and classify coding regions of transposable elements withingenomes. Going beyond the level of Ty1/copia and Ty3/gypsy superfamilies, it enables moredetailed and universally applicable classiﬁcation of LTR-retrotransposons in higher plant
genomes. Compared to previous computational tools, DANTE reﬁnes the annotation process
to reveal lineage-speciﬁc distribution patterns of LTR-retrotransposons along assembled
chromosomes.
The DANTE_LTR tool is designed to analyze output from the DANTE pipeline to identify
complete LTR retrotransposons, including structural features of retrotransposons such as LTR
sequences, primer binding sites, and target site duplications.
The TideCluster tool provides a solution for tandem repeat identiﬁcation in genome assemblies.
It employs TideHunter (Gao et al. 2019) to detect tandem repeats, and performs further
processing of the identiﬁed repeats by their similarity-based clustering and reconstructing
consensus sequences using Tandem Repeat Analyzer (TAREAN).
These tools provide robust and detailed analyses of nucleotide sequences of varying lengths,
from complete chromosome assemblies to sequences of only a few hundred base pairs. They
generate GFF3-formatted ﬁles containing sequence coordinates of annotated regions, which
can be visualized on the RepeatExplorer server using the JBrowse genome browser or
downloaded for further analysis. The combination of these tools on the RepeatExplorer server
enables comprehensive repeat annotation of genome assemblies.
References:Gao, Y., B. Liu, Y. Wang, and Y. Xing, 2019 TideHunter: eﬃcient and sensitive tandem repeat
detection from noisy long-reads using seed-and-chain. Bioinformatics 35: i200–i207.

55

Plant Chromosome Biology: Cytogenetics meeting 2023

Session 3, Talk, 18:00-18:20

38.
Unveiling the Nano-World of Plant Chromosomes: Chromatin
Fiber Compaction and Scaffold Protein Localization using
Advanced Microscopy Techniques
Professor Dr Nobuko Ohmido1, Dr Channarong Sartsanga1, Dr Rinyaporn Phengchat1,
Dr Toshiyuki Wako2, Dr Astari Dwiranti3, Professor Dr Kiichi Fukui4
1. Graduate School of Human Development and Environment, Kobe University
2. Institute of Crop Sciences, National Agriculture and Food Research Organization
3. Department of Biology, Faculty of Mathematics and Natural Sciences, University ofIndonesia
4. Graduate School of Pharmaceutical Sciences, Osaka University
Recent advancements in microscopy have revolutionized the analysis of intricate
structures at the nano level. In this study, we employed cutting-edge microscopes suchas the helium ion microscope (HIM), focused ion beam scanning electron microscope(FIB/SEM), high voltage transmission electron microscope (HVTEM), and ultra-HVTEM
with exceptional resolutions to delve into the plant chromosome structure. Theseadvanced tools oﬀer high magniﬁcation and contrast properties, enabling us to visualize
condensed metaphase chromosomes surface and investigate the precise localization of
scaﬀold proteins within.
Our study speciﬁcally focuses on the surface structure of barley metaphase
chromosomes, employing the HIM to estimate the unit size of chromatin ﬁber
compaction. Additionally, we explore the mechanism of chromosome condensation by
examining the eﬀects of Ca2+ depletion using the SEM. Furthermore, we demonstrate
the distribution of an important scaﬀold protein, Topoisomerase II (TopoII), in speciﬁcregions of the barley chromosomes using immunogold staining and HVTEM. Ourﬁndings reveal that TopoII proteins are distributed along the chromosome arms, withheightened density observed at the centromere and nucleolar organizing regions(NORs). We have achieved a comprehensive understanding of the precise alignmentand quantiﬁcation of TopoII protein at the nano level in barley chromosomes.

56Plant Chromosome Biology: Cytogenetics meeting 2023

Session 3, Talk, 18:20-18:40

39.
Wheat-rice hybrid mitochondria in Oryza wheat and theirtransmission to the next generation
Dr. Tety Maryenti1, Dr. Shizuka Koshimizu2, Ms. Nonoka Onda1, Dr. Takayoshi Ishii3, Dr.
Kentaro Yano4, Dr. Takashi Okamoto1
1. Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan
2. Department of Informatics, National Institute of Genetics, Shizuoka, Japan
3. Arid Land Research Center, Tottori University, Tottori, Japan
4. Department of Life Sciences, Meiji University, Kanagawa, Japan
In vitro fertilization (IVF) system has been established in rice, wheat and maize, andcombination of these three IVF systems oﬀers the possibility of artiﬁcially generatinginter-subfamily zygotes among three crops. We produced wheat–rice hybrid zygotes
via IVF with various gamete combinations, and allopolyploid zygotes consisting of awheat egg cell, a rice egg cell and a wheat sperm cell (ReWsWe zygotes), or wheat egg
cell, a rice egg cell, a wheat sperm cell and a rice sperm cell (Double zygote, DZ)
developed into mature plants. The hybrid nature of these possible wheat-rice hybrids
was addressed by FISH-based cytogenetical analyses and genome sequencing. The
results indicated that rice chromosomes are eliminated during the development ofallopolyploid wheat-rice zygotes, and that the ReWsWe zygote- and DZ-derived plants
possess a "wheat" nuclear genome and a "wheat" + "rice" mitochondrial genome. In
addition, the inserted rice mitochondrial DNA regions were transmitted to progenies.
Oryzawheat, the ﬁrst hybrid wheat possessing a heterogeneous cytoplasm acrosssubfamilies, can provide a new horizon for utilizing inter-subfamily genetic resources
between wheat and rice.

57

Plant Chromosome Biology: Cytogenetics meeting 2023

Session 3, Posters, September 11

Session 3
New tools, perspectives and applications
Posters58

Plant Chromosome Biology: Cytogenetics meeting 2023

Session 3, Posters, September 11

40.
The application laboratory for agricultural research at theCentre of Plant Structural and Functional Genomics ofInstitute of Experimental Botany
Mgr. Tereza Šlajsová1, Ing. Radim Čegan, Ph.D.1, RNDr. Jan Šafář, Ph.D.1
1. Institute of Experimental Botany AS CR, v. v. i., Centre of Plant Structural andFunctional Genomics
The Centre of Plant Structural and Functional Genomics of the Institute of Experimental
Botany in Olomouc established the Application Laboratory (AL) in 2017 as the ﬁrst
laboratory of its kind in the Czech Republic. It was founded within The Czech Academyof Sciences initiative called Strategy AV21 and its research programme Foods for the
Future. This programme aims to contribute to food safety through agricultural research.
The primary mission of this laboratory is to connect researches with plant breeders andcommercial companies. It can enhance competitiveness of the breeder companies
through transmission of the scientiﬁc knowledge and experience with modern methods
in molecular biology and genomics. This collaboration is fulﬁlled at diﬀerent levels. The
AL provides professional consultation, organisation of specialized workshops andpractical courses, as well as custom services. These include next generation sequencing,genotyping, ﬂow cytometry, molecular cytogenetics, bioinformatics and data analysis,
speciﬁc marker development and other comprehensive DNA analysis.
Acknowledgement: Work of the laboratory is funded by Strategy AV21, Programme
Foods for the Future (Period: 2020–2024).

59

Plant Chromosome Biology: Cytogenetics meeting 2023

Session 3, Posters, September 11

41.
Computational identiﬁcation of evolutionary conserved noncoding RNAs
Mgr. Petr Fajkus, PhD.1, Inž. Mgr. Agata Kilar, PhD.2
1. CEITEC Masaryk university, Institute of biphysics ASCR
2. CEITEC Masaryk university
Telomerase RNA (TR) is an important non-coding RNA that plays a crucial role in thesynthesis of telomere repeats and the assembly of the telomerase ribonucleoprotein
complex. However, characterizing TRs is challenging due to their highly variable nature.
Recent studies have successfully characterized TRs in various organisms, including
plants, algae, protists, and the insect order Hymenoptera (Fajkus NAR 2019, 2021,2023). To overcome the diﬃculties in identifying these mysterious RNAs acrossdiﬀerent taxonomic groups, we have optimized strategies.
Traditional methods, such as blast-based searches, are ineﬀective in identifying TR
homologs due to their low sequence conservation. However, using the Infernal tool,
which employs sequence-structure homology searches, signiﬁcantly improves theidentiﬁcation process on a broader evolutionary scale. Nevertheless, Infernal requires
more advanced procedures and programming skills compared to user-friendly webbased tools like blast. To address this issue, we have developed a user-friendly pipeline
for performing Infernal analyses. The pipeline only requires two inputs from the user:
query sequences in Stockholm format and a subset of NCBI genome assemblies as a
database. The results are automatically processed and presented in a comprehensive
table, including signiﬁcant hits and the taxonomy of the organisms.
Since Infernal is central to this analysis, these searches are particularly suitable for
identifying homologs of structural non-coding RNAs in a broad evolutionary context.
In line with T. Dobzhansky's statement, "Nothing in Biology Makes Sense Except in theLight of Evolution," we present a computational pipeline that simpliﬁes the search for
non-coding RNAs.
Funding: GAČR 20-01331X

60

Plant Chromosome Biology: Cytogenetics meeting 2023

Session 3, Posters, September 11

42.
Detection of protein recruitment and protein-protein
interactions at DNA lesions in plant protoplasts
Mgr. Martina Nešpor Dadejová, PhD.1, Mgr. Michal Franek, PhD.1, Mgr. MartinaDvořáčková, PhD.1
1. Mendel Centre for Plant Genomics and Proteomics, Central European Institute ofTechnology (CEITEC), Masaryk University
Plants are sessile organisms that require to adapt to constantly shifting environmental
conditions and face numerous exogenous and endogenous factors that damage their
DNA and lead to genetic alterations. However, the range of available tools forinvestigating the repair processes in plant genomes is limited.
Recently, we have adapted an experimental system that enables us to target DNA
lesions in the root cells and protoplasts of Arabidopsis thaliana (Nešpor Dadejová et al.,2022). Using this approach builds upon previous studies conducted on mammalianmodels we can transiently transform plant protoplasts with proteins of interest,
including DNA repair proteins, and consequently use laser irradiation to observe protein
recruitment within the nucleus and nucleolus. By employing this method, we can study
the dynamic nature of DNA repair in plants following exposure to UV irradiation andobserve alterations in protein interactions following DNA damage. Although we initiallytested this technique in Arabidopsis thaliana, its applicability can be extended to crop
plants, which holds signiﬁcant implications for practical ﬁeld applications.
Currently, we are expanding our methodologies to explore the impact of elevatedtemperatures, chemical agents such as zeocin, and CRISPR-Cas -induced DNA damageon the localization of DNA repair proteins within plant cells. This work opens up new
avenues for studying DNA damage response in plants and provides new insights into
the subject.

61

Plant Chromosome Biology: Cytogenetics meeting 2023

Session 3, Posters, September 11

43.
High-ﬁdelity repeat consensus sequences from short reads
Ludwig Mann1, Kristin Balasch1, Tony Heitkam1
1. Faculty of Biology, Technische Universität Dresden, D-01069 Dresden, Germany
Despite the many cheap and fast ways to generate genomic data, good and exact
genome assembly is still a problem, with especially the repeats being vastly
underrepresented and often misassembled. As short reads in low coverage are alreadysuﬃcient to represent the repeat landscape of any given genome, many read cluster
algorithms were brought forward that do repeat identiﬁcation and classiﬁcation. But
how can trustworthy, reliable and representative full-length repeat consensuses bederived from unassembled genomes? Here we combine methods from repeat
identiﬁcation and genome assembly to derive these robust consensuses. We test
several use cases, such as (1) consensus building from clustered short reads of nonmodel genomes, (2) from genome-wide ampliﬁcation setups, and (3) speciﬁc repeatcentered questions, such as the linked vs. unlinked arrangement of ribosomal genes. In
all our use-cases, the derived consensuses are robust and representative. To evaluate
overall performance, we compare our high-ﬁdelity repeat consensuses to
RepeatExplorer2-derived contigs and check if they represent real transposable
elements as found in long reads. Our results demonstrate that it is possible to generate
useful, reliable and trustworthy consensuses from short reads by a combination fromread cluster and genome assembly methods in an automatizable way. We anticipate
that this opens the way towards more eﬃcient and less manual repeat characterization
and annotation, beneﬁtting all genome studies, but especially those of non-modelorganisms.

62

Plant Chromosome Biology: Cytogenetics meeting 2023

Session 3, Posters, September 11

44.
Development of novel CRISPR/Cas9-based tools forvisualizing genomic sequences
Mr Bhanu Prakash Potlapalli1, Dr Andreas Houben1, Dr Jörg Fuchs1, Dr Nobuko
Ohmido2
1. Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)
2. Graduate School of Human Development and Environment, Kobe University
The DNA within the nucleus is intricately folded, and visualizing the three-dimensional
structure of the genome directly contributes to our understanding of how chromatin is
spatially organized and its role in gene expression during normal development anddisease. CRISPR-FISH provides a distinct advantage over traditional FISH methods as
it eliminates the need for complete DNA denaturation and maintains the inherent
chromatin structure. CRISPR-FISH uses target-speciﬁc crRNA, ﬂuorescence-labeledtracrRNA, and recombinant dCas9 protein to detect repetitive sequences in ﬁxed plant
and animal nuclei and chromosomes treated with formaldehyde or ethanol-acetic acid.
Using speciﬁc target-speciﬁc crRNAs and varying ﬂuorescence-labeled tracrRNAs,
diﬀerent DNA sequences can be selectively labeled. Additionally, this technique can be
combined with immunostaining and DNA replication methods to gain further insights.
Here we report on our recently developed method called CRISPR-CID (CRISPR/dCas9
mediated chromogenic in situ detection) that combines chromogenic signal detection
using alkaline phosphatase or peroxidase enzymes with CRISPR-based imaging.
CRISPR-CID applies the horseradish peroxidase enzyme for non-ﬂuorescently labelingof repetitive sequences in ﬁxed nuclei and chromosomes. The resulting chromogenic
signals can be analyzed using a conventional bright ﬁeld microscope. This technique isparticularly valuable in educational institutions and science outreach settings that have
limited resources and lack access to expensive ﬂuorescence microscopes. Furthermore,
we have improved the CRISPR-FISH method by introducing an ALFA-tag fused torecombinant dCas9 protein, resulting in improved signal intensity. We demonstratetarget-speciﬁc labeling using an ALFA-tagged dCas9 protein combined with acentromere-speciﬁc gRNA from A. thaliana and a ﬂuorescence-labeled NbALFA
nanobody. Additionally, we achieved enhanced signal intensity of target-speciﬁc signals
by utilizing a dCas9 protein that contains multiple copies of the ALFA-tag. This was
accomplished by combining it with a minibody and a ﬂuorescence-labeled anti-rabbit
secondary antibody. The development of a CRISPR-EM strategy for labelling repeatsthat can be analyzed at the highest resolution by transmission electron microscopy isin progress.

63Plant Chromosome Biology: Cytogenetics meeting 2023

Session 3, Posters, September 1145.
Reversing ancient chromosomal rearrangements in
Cardamine hirsuta (Brassicaceae) using CRISPR/Cas
Mgr. Petr Janás1, Mgr. Milan Pouch1, RNDr. Terezie Mandáková, Ph.D.1, prof. Mgr.
Martin Lysák, Ph.D., DSc.1
1. Central European Institute of Technology, Masaryk University, Brno, Czech Republic
Large-scale chromosomal rearrangements, including deletions, inversions, andreciprocal translocations, have played important roles in plant genome evolution andspeciation. By engineering these rearrangements, we can gain valuable insights into themolecular basis and impact of chromosomal aberrations on genotype and phenotype.
Here, we employed CRISPR/Cas technology to induce gross chromosomal
rearrangements in the genome of hairy bittercress (Cardamine hirsuta, Brassicaceae; n= 8), a widely used model organism to study various aspects of developmental
processes, ecological interactions, and evolutionary adaptations. By Agrobacteriummediated ﬂoral dip transformation using a transfer vector carrying SaCas9 driven by an
egg-cell-speciﬁc promoter and two highly speciﬁc gRNAs, we successfully generated
primary transformants in the T1 generation. PCR analysis and subsequent Sanger
sequencing conﬁrmed the presence of a 3-kb deletion and inversion within
chromosome Ch8, as well as 0.1 to 2-Mb reciprocal translocations between
chromosomes Ch6 and Ch8. These initial results highlight the eﬀectiveness of
CRISPR/Cas tools in manipulating chromosomal structures in C. hirsuta. They provide
the basis for further generation of chromosomal rearrangements, reversing modern
karyotypes back to their ancestral states, and understanding the eﬀects of theserearrangements.

64Plant Chromosome Biology: Cytogenetics meeting 2023

September 12, 8:30-11:10

Session 4
Mitosis, meiosis, gamete formation,
polyploidy and apomixes
Talks:

65

Plant Chromosome Biology: Cytogenetics meeting 2023

Session 4, Talk, 8:30-8:55

46.
Comparative genomics of plant centromeres
Jiri Macas1
1. Biology Centre, Czech Academy of Sciences
Centromeres represent the ﬁnal frontiers of genomics because of their high content ofsatellite repeats, which in principle are extremely diﬃcult to assemble. However, therecent introduction of accurate long-read sequencing technologies and advanced
assembly strategies has led to gapless assemblies of multiple plant genomes, usheringin a new era in centromere research. Although comparison of centromere sequences
between phylogenetically distant species is invaluable in revealing overall centromere
diversity in plants, it may not be as eﬃcient in elucidating individual stages or
evolutionary steps that led to their current variation. In principle, this type of
information is only available through the comparative analysis of closely related
genotypes, whose conserved synteny can be used as a reference for revealing shifts incentromere positions, changes in associated epigenetic proﬁles, and the accumulation
or elimination of centromeric repeats. This information can in turn be used to elucidate
general patterns and associated molecular mechanisms of centromere evolution. In thistalk, I will provide an overview of recent advances in comparative genomics ofcentromeres between multiple genotypes of extensively studied models or crops suchas Arabidopsis, rice, and maize, made possible by the availability of pangenome
assemblies in these species. I will then report on our eﬀorts to establish comparative
centromere (cyto)genomics in the legume tribe Fabeae which is of particular interest
because of the high sequence diversity and evolutionary dynamics of its centromeres.

66

Plant Chromosome Biology: Cytogenetics meeting 2023

Session 4, Talk, 8:30-9:15

47.
Cytogenetic and molecular evidence for polyclonality andsexual events in allopolyploid apomictic species Hieracium
halleri (Asteraceae)
Begoña Quirós-de-la-Peña1, Ladislava Paštová2, Jindřich Chrtek1, Eliška Záveská3, YannJ. K. Bertrand1, Jiřina Joseﬁová2, Barbora Tomešová2, Pavel Zdvořák4, Alexander
Belyayev2, Patrik Mráz4
1. Institute of Botany, Czech Academy of Sciences; Department of Botany, Faculty of
Science, Charles University
2. Institute of Botany, Czech Academy of Sciences
3. Institute of Botany, Czech Academy of Sciences; Department of Botany, Universityof Innsbruck
4. Department of Botany, Faculty of Science, Charles University
Hieracium s.str. (Asteraceae) is a highly diverse genus known for its notorious taxonomic
complexity, which is caused by widespread past interspeciﬁc hybridization. This process
is closely linked to polyploidization and apomixis (asexual reproduction by seeds), which
has ensured the persistence of otherwise sterile hybrids. As a result, apomictic
polyploid species dominate the taxonomic diversity of the genus. However, very little
is known about the evolutionary and biogeographical history of polyploid apomictic
species.
This study aims to decipher the evolutionary origin of a high mountain apomictic H.
halleri which probably arose from hybridization between H. alpinum and H. intybaceum.
To achieve this aim, we have applied a combination of cytogenetic (FISH and GISH),
ﬂow cytometric (assessment of mode of reproduction) and molecular approaches(RADSeq) on plants collected across the range of the species (the Alps and the Western
Carpathians).
Our results show that prevailing triploid H. halleri cytotype contains two genomes of H.
alpinum and one genome of H. intybaceum, the pattern explaining much closer
morphological aﬃnity of H. halleri to H. alpinum. We further found that despite strictly
apomictic mode of reproduction, H. halleri is cytogenetically variable taxon, both inchromosome number (prevailing are triploids, tetraploids are very rare) and karyotype
pattern (variation in number and positions of 5s rDNA, 45S rDNA and HintCL-82
repetitive DNA clusters, and unbalanced translocations). These results along with
RADseq data clearly indicate a polyclonal character of this hybridogenous species andsigns of probably ancient sexual reproduction (meiotically driven intergenomictranslocations). We suppose that both multiple origin of H. halleri and posthybridization
chromosomal rearrangements have been involved in rather unexpected chromosomal
and molecular variation of this apomictic species.

67Plant Chromosome Biology: Cytogenetics meeting 2023

Session 4, Talk, 9:15-9:35

48.
Spatial in vivo dynamics of mitotic divisions in barley(Hordeum vulgare)
Dr. Ales Pecinka1, Mgr. Katerina Kaduchova1, Dr. Cintia Marchetti2, prof. Miroslav
Ovecka2, Dr. Petr Galuszka2, Dr. Véronique Bergougnoux2, prof. Jozef Šamaj2
1. Institute of Experimental Botany, Olomouc, Czech Republic
2. Palacky University, Olomouc, Czech Republic
The structure and the dynamics of chromatin organization in cell nuclei are not strict
and may change rapidly during the cell cycle, in diﬀerent tissues, and in response toabiotic and biotic stimuli. The most rapid changes in cell architecture occur during cell
divisions. In mitosis, the chromatin arrangement is changed due to its condensation into
compact chromosomes, which are subsequently distributed into the newly emerging
daughter cells. To study the dynamics of mitosis in plants with large genomes, wedeveloped a series of unique barley marker lines carrying ﬂuorescently labeled fusion
proteins that are indicative of speciﬁc chromosomal/nuclear domains such as thechromatin (GFP/YFP/CFP-H2B), microtubules (mCHERRY-TUA3) and nucleolus (YFPFIB1). With these lines, we were able to measure the length of mitotic division in barleyroot cells and reveal the dynamics of tagged cellular structures. Moreover, we foundthat the condensation of mitotic chromosomes does not reach its maximum in
metaphase but proceeds until telophase where the newly formed daughter cells
emerge.
Funding by the Czech Science Foundation project 21-02929S.

68

Plant Chromosome Biology: Cytogenetics meeting 2023

Session 4, Talk, 9:35-9:55

49.
Unraveling the Rosa canina Genome: Cytogenetic, Genomic,
and Phylogenetic Insights into Pentaploid Genome
Harbouring Asymmetrical Meiosis.
Jana Lunerová1* (1st speaker) and Veit Herklotz2** (2nd speaker), Radka Vozárová1, André Marquez3,
Meng Zhang 3, Bruno Hüttel3, Andreas Houben4, Joerg Fuchs3, Dörte Harpke 4, Christiane M. Ritz2 andAleš Kovařík1
1. Department of Molecular Epigenetics, Institute of Biophysics, Czech Academy of Sciences, v.v.i.,
Královopolská 135, 612 00 Brno, Czech Republic
2. Department of Botany, Senckenberg Museum of Natural History Görlitz, Am Museum 1, D-02826,
Görlitz, Germany
3. Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-vonLinné-Weg 10, 50829 Cologne, Germany
4. Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstraße 3, 06466 Gatersleben,
Germany* jana.luner@ibp.cz** veit.herklotz@senckenberg.de
Polyploidy and hybridisation often have profound consequences on the reproductive strategy in plants.
An intriguing example represent the odd ploid (2n = 5x = 35) dogroses with their distinctive hemisexual
meiosis, diﬀerentiating between pairing bivalents, inherited by pollen and egg cells, and non-pairing
univalents transmitted by egg cells only.
Here, we combined cytogenetic, phylogenetic, and genomic approaches to analyse dogrose genomes.
Using FISH (ﬂuorescence in situ hybridisation) we investigated chromosomes in male canina meiosis ofseveral dogrose species. In meiotic phase I we found diﬀerences in the distribution of rDNA and satellite
markers between bivalent and univalent chromosomes. All cytogenetic markers could be successfully
mapped to the newly developed whole genome assembly of R. canina (sequenced by the PacBio HiFi
technology) and their distribution and abundance was well correlated with FISH results. The synteny
analysis (SyRi) revealed numerous sizeable inversions, deletions, and other rearrangements on univalentssuggesting a possible connection to their non-pairing nature and unique evolutionary trajectories. In
addition, the pollen's single-copy loci originating from the two bivalent-forming chromosome sets (2x)exhibited extremely high levels of homology. The remaining three sets showed signiﬁcant dissimilarityand likely originated from univalent-forming chromosomes. Phylogenetic analyses using diploid rose
species revealed that in R. canina two bivalent (homologous) and one univalent forming subgenomesalign with the Synstylae clade (named accordingly the “S-type” subgenome) while the remaining two
univalent forming genomes have their origin in the Rosa clade (“R-type” subgenome). The genomic
composition of 5x R. canina can thus be tentatively written as “SSsRR”. In conclusion, through combined
methodical approaches we hope to provide a deeper understanding of the unique meiotic behaviour ofchromosomes in R. canina and its allies.
Funding:German Science Foundation (DFG Ri2090/3-1, 4-1)
Czech Science Foundation (GACR 10-14133J)

69

Plant Chromosome Biology: Cytogenetics meeting 2023

Session 4, Talk, 9:55-10:15

50.
The protein-protein interaction network of KNL2 in
Arabidopsis thaliana
Dr Inna Lermontova1, Manikandan Kalidass1, Maryia Ratnikava1, Dr Samuel Le Goﬀ Le
Goﬀ2, Aline Probst, Dr.2, Prof Klaus D Grasser3
1. Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben,
Corrensstrasse 3, D-06466 Seeland, Germany
2. GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001 Clermont–
Ferrand, France
3. Cell Biology and Plant Biochemistry, Biochemistry Center, University of Regensburg,
Universitätsstraße 31, D-93053, Regensburg, Germany
Centromeres are chromosomal regions where kinetochore proteins interact and form aprotein complex that regulates the cell cycle. The licensing of CENH3 to thecentromeres is regulated by the kinetochore protein KNL2 in plants and otherorganisms. In this work, we aim to elucidate and characterize the regulatory factors thatinteract with KNL2, which will aid in determining the functional role of KNL2 in
Arabidopsis. Immunoprecipitation combined mass spectrometry (IP-MS) and yeast-two
hybrid (Y2H) library screening performed with full-length and N- and C-terminal partsof KNL2 resulted in identiﬁcation of 37 proteins from the ubiquitination andsumoylation pathways. Initially, three proteins, UBC19, UBC20 (ubiquitin-conjugating
enzymes), and ULP1D (a deSUMOylating factor), were selected from the Y2H library
screening as a putative direct interactor of KNL2. The interaction of these proteins has
been validated using BiFC interaction analysis in N. benthamiana. UBC19 and UBC20
interact directly with KNL2 and KNL2-N after applying MG115, which aligns with theprevious results showing that KNL2 is regulated by the proteasome degradation
pathway at its N-terminal part. The interaction of ULP1D and UBC19 with KNL2-C has
been shown, which is evident that the level of KNL2 in the mitotic cell cycle (metaphaseto anaphase) could be regulated via the SUMO-ubiquitin crosstalk pathway. Further,
we identiﬁed that the lysine sites (336K and 339K) of KNL2 are the target sites forbinding ubiquitin protein through interaction and localization analysis. Thus, the KNL2
protein is regulated via the degradation pathways for the proper cenH3 loading and cell
division processes.

70Plant Chromosome Biology: Cytogenetics meeting 2023

Session 4, Talk, 10:15-10:35

51.
Single pollen nucleus genotyping and virus tools for meiotic
gene studies in barley (Hordeum vulgare L.)
Suriya Tamilselvan Nattar Amutha1
1. IPK Gatersleben, Germany
Meiotic recombination generates genetic variation through reciprocal (crossover, CO)and non-reciprocal (gene conversion, GC) DNA exchanges between homologous
parental chromosomes. Typically, COs are positioned towards distal regions ofchromosomes, especially in crops with large genomes like barley leaving large portionsof the genome untapped during breeding. Therefore, to accelerate barley breeding,novel approaches are required to achieve the desired genetic recombination outcome.
We present here multiplex Crystal digital PCR (dPCR)-based single pollen nucleus
genotyping for rapid and high throughput assessment of recombination rate as well as
CO interference in genetically linked chromosomal intervals in barley hybrids. We used
our dPCR approach to measure an increase in male meiotic recombination rate in hybridbarley defective for the anti-CO factor HvRECQ4 (ATP-dependent DNA helicase).
Moreover, natural variation in male meiotic recombination rates in hybrid barley wasassessed. For targeted gene editing and transient transcript downregulation in barley,
we employed Barley stripe mosaic virus (BSMV)-mediated virus-induced gene editing(VIGE) and virus-induced gene silencing (VIGS) strategies, respectively. Heritably editedbarley plants defective for key meiosis genes were isolated using VIGE. In sum,multiplex Crystal dPCR and VIGE/VIGS approaches enable rapid dissection of meiotic
gene function in barley and likely also other crops.

71Plant Chromosome Biology: Cytogenetics meeting 2023

Session 4, Talk, 10:35-10:55

52.
Dynamics and adaptation of the meiotic recombination
landscape among natural and artiﬁcial chromosomes inholocentric Rhynchospora plant species
Stefan Steckenborn1, Meng Zhang1, Magdalena Marek1, Bruno Hüttel1, Andre
Marques1
1. Max Planck Institute for Plant Breeding Research
The meiotic recombination landscape is highly inﬂuenced by chromosome number, as
at least one crossover per chromosome occurs in most plants. Additionally, centromeres
typically inhibit meiotic recombination, driving crossover formation towards
chromosome ends. Therefore, holocentric plant species, with hundreds of centromere
units distributed across the length of each chromosome, oﬀer a unique opportunity to
study how atypical centromeres can aﬀect the meiotic recombination landscape.
Moreover, due to their high tolerance to chromosome ﬁssions and fusions, the genome
structure within holocentric plant species is highly dynamic, oﬀering an appealing
alternative to analyze the major eﬀects of sudden changes in chromosome number via
ﬁssion and fusions (either naturally evolved, or artiﬁcially generated by DNA damage
and Cas9-mediated chromosome engineering) on crossover frequency and distribution.
The present project describes how we adapted a methodology of single-cell RNA/ATAC
sequencing to build recombination maps using form thousands of pollen nuclei, withthe aim of uncovering the diﬀerences in CO landscape and revealing the major eﬀects
of karyotype evolution on recombination dynamics in non-monocentric organisms.

72

Plant Chromosome Biology: Cytogenetics meeting 2023

Session 4, Talk, 10:55-11:10

53.
STED nanoscopy of intra-nuclear chromatin structures inbarley (Hordeum vulgare L.)
Mgr. Veronika Kolačková, Ph.D.1, Mgr. Alžběta Doležalová, Ph.D.1, Mgr. Ivan Novotný,Ph.D.2, Mgr. Eva Hřibová, Ph.D.1
1. Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant
Structural and Functional Genomics
2. Institute of Molecular Genetics of the Czech Academy of Sciences, Light Microscopy
Group
Recent development in the ﬁeld of super-resolution microscopy enabled detailed
analysis of cellular or even sub-cellular structures. One of the super-resolution
techniques, stimulated emission depletion (STED) microscopy, is based on confocal
method and provides an ability to achieve spatial resolution in the range of 30 – 80 nm.
However, STED microscopy is extremely sensitive to refractive index mismatch along
the optical path. Any mismatch can result in spherical aberrations leading to asigniﬁcant reduction in resolution and signal loss. Moreover, the combination of
excitation laser and STED laser causes fast ﬂuorophore bleaching, thus speciﬁc highly
stable ﬂuorophores have to be used.
In order to fully utilize the potential of STED analysis in plant chromatin research,
we optimized the whole procedure of sample preparation and image acquisition. We
used barley (cv. Morex) as model plant to provide a protocol useful for detailed analysisof chromatin structure and organization in highly condensed mitotic metaphase
chromosomes and interphase nuclei. To achieve the best sample purity and subsequent
resolution, mitotic metaphase chromosomes as well as interphase nuclei were isolated
by ﬂow sorting. Pure chromosomes or nuclei were embedded in polyacrylamide gel topreserve their three dimensional (3D) structure. The eﬀect of diﬀerent commerciallyavailable mounting media was studied after 3D-FISH experiments with probes labelled
by Abberior STAR 580 and 635P, and chromatin visualization by SPY650-DNA. Our
optimized protocol enabled to achieve lateral resolution of ~ 30 – 40 nm in the 3D
samples, and to observe unique structure and arrangement of chromatin ﬁbers in the
3D space of interphase nuclei and mitotic chromosomes.

73Plant Chromosome Biology: Cytogenetics meeting 2023

Session 4, Posters, September 12

Session 4
Mitosis, meiosis, gamete formation,
polyploidy and apomixes
Posters:74

Plant Chromosome Biology: Cytogenetics meeting 2023

Session 4, Posters, September 12

54.
Both male and female meiosis contribute to non-Mendelian
inheritance of parental chromosomes in interspeciﬁc planthybrids (Lolium × Festuca)
Mgr. Jana Szecówka, Ph.D.1, Mgr. Joanna Majka, Ph.D.1, Mgr. Marek Glombik, Ph.D.2,
Doc. David Kopecký, Ph.D.1
1. Institute of Experimental Botany, CAS, Olomouc, CZ
2. John Innes Centre, Norwich, UK
Elimination of chromosomes from one parental subset is a phenomenon occasionallyobserved in newly developed interspeciﬁc hybrids. This represents a limitation to thespeciation of allopolyploids and an obstacle for breeders who use wide hybridization
for crop improvement. The mechanisms underlaying uniparental genome elimination
are still poorly understood.
Using a cytogenetic approach, we studied the chromosome composition of F2 andreciprocal backcross (BC1) generations of Festuca x Lolium hybrids, commercially
important fodder and turf grass. We found that during female
meiosis, Festuca chromosomes are replaced by Lolium chromosomes, presumably by
the mechanism of meiotic drive. Occasional elimination of Festuca chromosomes was
also observed during male meiosis. Detailed analysis of the ﬁrst and second male
meiotic divisions revealed that Lolium univalents are regularly attached to microtubules
and transmitted to daughter nuclei, whereas Festuca univalents often remain
unattached and are subsequently eliminated.
Additionally, we performed meiotic transcriptome analysis and identiﬁed two
kinetochore genes, NNF1 and NDC80, expressed only from the Lolium variants in all
meiotic samples, while they were expressed from both genomes in somatic tissues. It is
plausible that the elimination of the Festuca chromosomes in the hybrid is aconsequence of the silencing of the Festuca alleles of the kinetochore genes leading to
improper kinetochore complex assembly on these chromosomes.
Our ﬁndings help to elucidate the mechanisms responsible for chromosome eliminationand genome dominance occurring in interspeciﬁc hybrids. They are relevant not only tothe research community but also to plant breeders to facilitate decision-making inparental line selection.

75

Plant Chromosome Biology: Cytogenetics meeting 2023

Session 4, Posters, September 1255.
ZIP4 is required for normal progression of synapsis and forover 95% of crossovers in wheat
Dr Azahara C. Martin1, Mrs Tracie N. Draeger2, Prof. Graham Moore2
1. Institute for Sustainable Agriculture (IAS-CSIC), Córdoba, Spain
2. John Innes Centre, Norwich, UK
Tetraploid (AABB) and hexaploid (AABBDD) wheat possess multiple sets of similar
chromosomes (homeologs). Thus, the success of meiosis and fertility rely on synapsis
and crossover (CO) formation exclusively occurring between homologous
chromosomes (homologs). The major meiotic gene TaZIP4-B2 (Ph1) in hexaploid wheat
promotes homologous COs while suppressing homeologous COs. In otherspecies, ZIP4 mutations eliminate approximately 85% of COs, consistent with loss ofthe class I CO pathway. Tetraploid wheat has three ZIP4 copies: TtZIP4-A1 on
3A, TtZIP4-B1 on 3B, and TtZIP4-B2 on 5B. We show that disrupting two ZIP4 copies
in Ttzip4-A1B1 double mutants reduces COs by 76-78%, while disrupting all threecopies in Ttzip4-A1B1B2 triple mutants reduces COs by over 95%. This indicates thateither the numbers of class I COs in tetraploid wheat is higher than previously reported,or that the TtZIP4-B2 copy also aﬀect class II COs. It is possible that the duplication anddivergence of ZIP4 genes during wheat polyploidization have given TaZIP4-B2 anadditional function to stabilize both CO pathways. Moreover, in plants lacking all
three ZIP4 copies, synapsis is delayed and never completed. These ﬁndings
conﬁrm ZIP4-B2 (Ph1) essential role in synapsis, and indicate stronger eﬀects
of TtZIP4 genes compared to Arabidopsis and rice.

76

Plant Chromosome Biology: Cytogenetics meeting 2023

Session 4, Posters, September 1256.
Uncovering the mechanism of cold-induced meiotic
restitution in Musa spp.
Astrid Johanna Irena Severyns1
1. KU Leuven
Most banana cultivars currently grown are triploid, as these are desired for theirsuperior agronomical quality and high level of sterility leading to seedless fruits. As aresult of this, banana plants need to be propagated vegetatively, leading to large
monocultures with identical clones that are highly vulnerable to (a)biotic stress. One of
the solutions to guarantee sustainable banana production under changing
environments is the development of new cultivars that combine productivity of highquality fruits with adaptation to local climates. In current Musa breeding, new triploid
cultivars are created from existing ones via interploidy crossing. This breeding schedule
is however laborious and ineﬃcient. An alternative pathway to generating triploidbanana genotypes is the exploitation of sexual polyploidization via the ectopic
formation of diploid (2n) gametes. This would avoid ineﬃcient interploidy crosses andcomplex inheritance patterns. We have been able to induce 2n pollen grain formation
after a cold treatment of Musa velutina, and are using cytological techniques to uncover
the nature of the temperature-induced defect that is observed.

77

Plant Chromosome Biology: Cytogenetics meeting 2023

Session 4, Posters, September 12

57.
Recurrent plant-speciﬁc duplications of KNL2 and its
conserved function as a kinetochore assembly factor
Ramakrishna Yadala1, Sheng Zuo2, Fen Yang3, Ales Pecinka3, Inna Lermontova1
1. Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben,
Corrensstrasse 3, D-06466 Seeland, Germany
2. Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5,
CZ-625 00 Brno, Czech Republic
3. Institute of Experimental Botany, Czech Acad Sci, Centre of the Region Haná for
Biotechnological and Agricultural Research, Šlechtitelů 31, 779 00 Olomouc, Czech
Republic
KINETOCHORE NULL2 (KNL2) plays a key role in centromere recognition andkinetochore assembly. To gain insight into the origin and diversiﬁcation of the plant
KNL2 gene, we reconstructed its evolutionary history and classiﬁed into two clades;
αKNL2 and βKNL2 in eudicots and γKNL2 and δKNL2 in grasses, respectively. KNL2
proteins across species can be identiﬁed by the presence of conserved module called
SANTA (SANT Associated) domain. The presence of CENPC-k motif apart from the
SANTA domain diﬀerentiates αKNL2 and γKNL2 from βKNL2 and δKNL2. However,despite the absence of the CENPC-k domain, Arabidopsis βKNL2 exhibits centromeric
localization similar to αKNL2. Homozygous βknl2 mutants of Arabidopsis cannot
survive beyond the seedling stage, while heterozygous mutants with normal vegetative
growth have a high percentage of abnormally developed or aborted seeds. Defects inseed development are most likely not related to the formation of abnormal gametes but
to abnormalities in postzygotic cell divisions. To investigate the βKNL2 function and its
centromere targeting mechanism, we generated several truncated βKNL2 versions bydeleting the conserved motifs and domains. We hypothesize that centromeric
localization of βKNL2 is dependent on its interaction with other proteins which might
happen through SANTA domain and/or conserved motifs at the C-terminus. The
conﬁrmed centromeric localization of βKNL2 and mutant analysis suggests that it isinvolved in the loading of centromeric histone H3 CENH3 into centromeric
nucleosomes, similar to αKNL2. Overall, our study provides insight into theevolutionary diversiﬁcation of the KNL2 gene and its role in kinetochore assembly andmaintenance of genome stability.

78Plant Chromosome Biology: Cytogenetics meeting 2023

Session 4, Posters, September 12

58.
Identiﬁcation of novel meiotic players based on screening of
Axis TurboID candidates (ATC) and SUMO candidates
Baicui Wang1, Dr. Feng Chao1, Franziska Hartmann1, Jana Lorenz1, Dr. Maria Cuacos1,
Dr. Stefan Heckmann1
1. Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) OT Gatersleben
During meiosis, random assortment of homologous chromosomes and homologous
recombination leading to the formation of crossover (CO; reciprocal genetic exchange
between homologs) both contribute to the genetic diversity of the oﬀspring. The
formation of CO depends on the interplay between a proteinaceous structure called
the meiotic chromosome axis, the synaptonemal complex (SC) and meiotic
recombination proteins. In addition, posttranslational protein modiﬁcations (PTMs) playvital roles in dynamically regulating components of the axis, SC and the recombination
machinery.
Despite the key role of the meiotic chromosome axis and the SC for CO formation, acomplete picture of the underlying mechanisms and players is still missing. Recently,
TurboID-based proteomic proﬁling of the meiotic chromosome axis identiﬁed a list of
39 axis-proximate candidate proteins (ATCs) in Arabidopsis thaliana. Among them, both
known and new meiotic proteins are found. Here, male meiotic chromosome behavior
was studied in selected T-DNA insertion mutant lines and the candidate gene ATC3 wasfound to be required for meiosis, i.e. the formation of the obligate CO. Further initial
data on the functional role and the localization of ATC3 based on fusion proteins will
be presented.
Despite the essential role of PTMS in regulating axis, SC, and CO formation in nonplant species, our knowledge of SUMOylation’s involvement in plant meiosis is limited.
Hence, mutants for two SUMO genes, SUMO3 and SUMO5, were isolated based on
CRISPR in A. thaliana. Initial data on the localization of SUMO5 and SUMO3 based on
fusion proteins and of their mutant phenotypes will be shown.

79

Plant Chromosome Biology: Cytogenetics meeting 2023

Session 4, Posters, September 1259.
Anti- and pro-CO factors in barley
Maria Cuacos1, Mohammad Ayoub1, Suriya Amutha1, Franziska Hartmann1, Jana
Lorenz1, Nils Stein1, Goetz Hensel2, Jochen Kumlehn1, Stefan Heckmann1
1. Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)
2. Heinrich Heine University Düsseldorf
Meiosis is the cell division responsible for the generation of gametes. During meiosis,
homologous recombination ensures: 1) formation of a physical link between maternaland paternal chromosomes, essential for proper chromosome segregation and fertility;and 2) exchange of genetic information between parental chromosomes, assuring
genetic variability harnessed during breeding. The outcome of homologous
recombination can be either a crossover (reciprocal exchange of genetic material
between homologous chromosomes) or a non-crossover, and this is regulated byantagonistic actions of so-called “pro-crossover” and “anti-crossover” factors.
One limitation of plant meiotic homologous recombination, in particular in cereal crops
such as barley (Hordeum vulgare), is that crossovers do not occur homogeneously along
the genome. Instead, they form preferentially in (sub-)terminal chromosome regions,leaving large (peri-)centromeric regions unrecombined.
We are interested in better understanding meiosis in cereals, using barley as our model,
ultimately aiming to manipulate the frequency and/or distribution of recombination
events. We selected three meiotic candidates which have been reported in Arabidopsis
and other non-plant species as pro-crossover (HEI10) and anti-crossover factors (FIGL1
and RECQ4) for mutant generation and meiotic characterization. HEI10, as in otherspecies, is needed for crossover formation and its absence leads to mostly unpaired
chromosomes during meiosis; FIGL1, opposite to results in Arabidopsis, is needed forcrossover formation, being its role as anti-crossover factor still to be determined; andRECQ4 is an anti-crossover factor increasing recombination up to 4-fold in selected
chromosomal intervals.

80Plant Chromosome Biology: Cytogenetics meeting 2023

Session 4, Posters, September 12

60.
Tetraploid B. rapa are highly tolerant of tetravalent formation
and aneuploidy
Zhenling lyu1, Annaliese Mason1
1. Bonn University
Although turnip (Brassica rapa var. rapa) cultivars are usually diploid, autotetraploids
produced by artiﬁcially induced chromosome doubling are also grown as fodder crops,
where they are competitive with their (natural) diploid counterparts. To date, induced
autopolyploids in Brassica are all thought to have unstable meiosis, but the use of
autotetraploid as crops suggest high fertility and putatively meiotic stability. Hence, we
aimed to investigate genome structure, meiosis, and fertility in autotetraploid turnips.
We found loss and gain of individual chromosomes (aneuploidy) was common in
autotetraploid turnip lines sourced from germplasm banks. Meiotic conﬁgurations(number of univalents, bivalents, trivalent, tetravalent, and higher multivalents per cell)were quantitatively assessed at the diakinesis stage, showing an average of 3.1 - 4.9
tetravalents and 7.2 - 9.6 bivalents per meiosis in this material. High pollen viability wasobserved in both euploids and aneuploids.
High frequencies of meiotic tetravalent formation and observations of aneuploidy
without major phenotypic eﬀects or reductions in pollen fertility indicate that tetraploid
B. rapa is highly tolerant of chromosomal variation, which may explain its success as acrop despite a lack of conventionally stable meiosis (fully diploidized/ 100% bivalent
formation). Possible mechanisms (structural and epigenetic factors) for this eﬀect areunder investigation.

81

Plant Chromosome Biology: Cytogenetics meeting 2023

Session 4, Posters, September 1261.
Antibodies against kinetochore proteins NDC80 and KNL1
provide highly versatile markers of centromeres in ﬂowering
plants (angiosperms)
Ludmila Oliveira1, Pavel Neumann1, Petr Novák1, Andrea Koblížková1, Jiří Macas1
1. Biology Centre CAS, Institute of Plant Molecular Biology, České Budějovice, Czechia
The positions of centromeres on mitotic chromosomes can be roughly determinedmorphologically as primary constrictions. However, accurate determination offunctional centromere domains depends on the detection of centromere-associatedproteins using speciﬁc antibodies. The most commonly used marker for centromeres isthe centromere-speciﬁc histone CENH3, which replaces the canonical histone H3 incentromeric nucleosomes. CENH3 is very similar to H3, except for the N-terminal tail,which is usually used as an immunogen to produce antibodies. Unfortunately, the Nterminus of CENH3 is highly divergent among species, resulting in the need to develop
CENH3 antibodies for each species or genus of interest, which is laborious and costly.
Recently, we developed antibodies against the kinetochore proteins NDC80 and KNL1
in Cuscuta species. Sequence analysis of the domains used as immunogens revealed ahigh degree of similarity across ﬂowering plants, suggesting that the antibodies
developed primarily for Cuscuta spp. may also work in other plant species. This was
conﬁrmed by in situ immunodetection of NDC80 and KNL1 in several eudicot, basal
dicot, and monocot species. Our ﬁndings open up possibilities for broader applicationsof the developed antibodies in studying centromeres across diverse plant species.

82Plant Chromosome Biology: Cytogenetics meeting 2023

Session 4, Posters, September 12

62.
Proteomic proﬁling of meiotic chromosome axis
in Arabidopsis thaliana based on TurboID
Chao Feng1, Elisabeth Roitinger2, Otto Hudecz2, Maria Cuacos1, Jana Lorenz1, Veit
Schubert1, Baicui Wang1, Rui Wang1, Karl Mechtler2, Stefan Heckmann1
1. Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) OT Gatersleben,
Seeland, Germany
2. Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna,
Austria; Institute of Molecular Biotechnology of the Austrian Academy of Sciences(IMBA), Vienna BioCenter (VBC), Vienna, Austria; The Gregor Mendel Institute of
Molecular Plant Biology of the Austrian Academy of Sciences (GMI), Vienna
BioCenter (VBC), Vienna, Austria

The meiotic chromosome axis is a proteinaceous structure along which sister
chromatids are arranged in a loop-base array during meiotic prophase I. The
chromosome axis is critical for synapsis and meiotic recombination. In plants, thelimited number of meiotic cells embedded in ﬂoral organs constrains proteomic
approaches aiming to unravel the composition and regulation of meiotic chromosome
axes.
Here we present the application of TurboID (TbID)-based proximity labeling in meiotic
cells of Arabidopsis thaliana for two meiotic chromosome axis-associated proteins
ASYNAPTIC1 (ASY1) and ASYNAPTIC3 (ASY3). Among 39 identiﬁed candidates most
known axis-related and novel proteins were identiﬁed. After mutant screening basedon meiotic chromosome spread analysis, we identiﬁed (at least) four of the novel
candidates with a meiotic mutant phenotype (presence of univalents, i.e. failure to form
the obligate CO). Among them, one candidate was found to be part of the synaptonemal
complex (SC). In its absence, SC formation is disrupted and chiasmata formation is
reduced while CO levels are increased and CO interference is virtually abolished.
Together, TbID-based proximity labeling is a robust tool for the identiﬁcation of protein
proximate proteins in rare cell types such as meiotic cells in A. thaliana.

83Plant Chromosome Biology: Cytogenetics meeting 2023

September 13, 8:30-10:05

Session 5
Specialized chromosomes(Sex chromosomes, B chromosomes and others)

Talks:

84

Plant Chromosome Biology: Cytogenetics meeting 2023

Session 5, Talk, 8:30-08:50

63.
Key drivers of plant sex chromosomes knowledge explosion
Roman Hobza, Václav Bačovský, Vojtěch Hudzieczek, Radim Čegan, Viktor Tokan,
Tomáš Janíček, Marcel Hubinský, Nicolas Blavet, Dmytro Abramov, Lucie Horáková,
Pavla Novotná, Markéta Bodláková, Bohuslav Janoušek, Jose Rodriguez, Boris Vyskot,Matěj Lexa, Pavel Jedlička, Marie Krátká, Zdeněk Kubát and Eduard Kejnovský
Department of Plant Developmental Genetics, Institute of Biophysics of the Czech
Academy of Sciences
For decades, we have been gradually accumulating data about sex chromosomes andtheir role in genome structure and evolution. Recent advances in NGS data mining,
microscopic analysis, epigenetics and functional genetics have signiﬁcantly accelerated
our knowledge about sex chromosomes. Our eﬀort to test long-standing hypothesis
and conﬁrm old theories should transform towards raising new biological questions. I
will brieﬂy summarize recent developments and the state of the art of sex chromosome
research.

This study was supported by a research grant from the Czech Science Foundation(grants no. 22-00301S, 21-00580S and 22-00364S).

85

Plant Chromosome Biology: Cytogenetics meeting 2023

Session 5, Talk, 8:50-09:10

64.
A complex affair – sex chromosome evolution in plants
Ing. Václav Bačovský, Ph.D.1, Ing. Radim Čegan, Ph.D.1, Mgr. Zdeněk Kubát, Ph.D.1,
Mgr. Lucie Horáková1, Ing. Pavla Novotná1, Mgr. Jana Kružlicová1, RNDr. Roman
Hobza, Ph.D.1
1. Department of Plant Developmental Genetics, Institute of Biophysics of the Czech
Academy of Sciences
Generally accepted theory predicts that the sex chromosomes evolved from a regularpair of autosomes. Through a series of chromosomal rearrangements and cycles ofdeleterious mutation accumulation, XY chromosomes gain diﬀerent function and diﬀer
in their (epi)genomic organisation leading to functional and structural diversity. Welldiﬀerentiated sex chromosome systems have evolved a core set of characteristics inanimals that are yet still to be fully explored in plants. We found that plant sex
chromosomes undergo large proto-sex chromosome-autosome rearrangements,
followed by the evolution of recombination suppression and partial/incomplete dosage
compensation. We suggest that epigenetic conﬂict within the non-recombining regionof the Y chromosome is predated by large-scale gene down-regulation that leads toexpression imbalances, either in one or both sexes. This process is accelerated by theaccumulation of transposable elements and satellites within the non-recombining
region as demonstrated in Silene latifolia and Rumex acetosa, or newly in R. hastatulus.
The sequence divergence and later morphological diﬀerences (heteromorphism) mightlead to co-evolution of similar mechanisms termed in animals as sex chromosome
meiotic inactivation. In this work, we show that the sex chromosomes are remarkable
examples of genomic convergence, although subsequent evolutionary steps are more
dependent on epigenetic state and evolutionary history of both sex chromosomes. We
show recent discoveries in four well-established plant species – Silene, Rumex,
Humulus and Coccinia, and discuss future directions of plant sex chromosome research.

86Plant Chromosome Biology: Cytogenetics meeting 2023

Session 5, Talk, 09:10-09:25

65.
Considerable genetic diversity within the hop varieties
explains non-Mendelian segregation patterns
Lucie Horáková1, Václav Bačovský1, Radim Čegan1, Pavla Navrátilová2, Jan Šafář2, Beáta
Strejčková2, Josef Patzak3, Roman Hobza1
1. Department of Plant Developmental Genetics, Institute of Biophysics of the Czech
Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic.
2. Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31,
783 71 Olomouc, Czech Republic.
3. Hop Research Institute Co. Ltd, Kadaňská 2525, 438 46 Žatec, Czech Republic.
Humulus lupulus is a dioecious and economically important plant classiﬁed into ﬁvevarieties - var. lupulus, lupuloides, pubescens, neomexicanus, and cordifolius. Thesevarieties have distinct levels of genetic variability following their geographical origin.
Despite the long breeding history of hop, genomic studies of male plants that are
essential for hop breeders were for a relatively long time neglected. Interestingly, wild
male hop displays non-Mendelian segregation patterns that lead to meiotic
abnormalities, and further genomic instability in subsequent generations. However, theorigin of such meiotic instability and the mechanism through which the new lines show
stable chromosome inheritance is still enigmatic.To explore the non-Mendelian
segregation in hop, we analyzed centromeric repeat fraction of hop genome using ChIPsequencing assay with Humulus lupulus-speciﬁc CENH3. This allowed us to identify
new chromosome-speciﬁc marker(s) (namely TR120 and cl293) that were used to study
chromosome segregation defects in mitosis and meiosis. Using ﬂuorescence in situ
hybridization we found unbalanced segregation patterns that leads to aneuploidy(2n=18-22) in the new generation. The unbalanced segregation pattern is caused
namely by dicentric chromosome that is lagging during transition from metaphase I toanaphase I. Our results show structurally diverse genomes of Humulus varieties andsuggest an inﬂuence of breeding and geographical isolation on evolution of hop
genome. These ﬁndings may help to improve new hop breeding programs tocharacterize new hop cultivars.

87Plant Chromosome Biology: Cytogenetics meeting 2023

Session 5, Talk, 09:25-09:45

66.
Does B chromosome alternate the pollen development in wildsorghum?
Mgr. Miroslava Karaﬁátová, Ph.D.1, Mgr. Magdaléna Malurová1, Mgr. Jan Bartoš, Ph.D.1
1. Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant
Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech
Republic
B chromosomes, dispensable genomic components of many species, are perceived as
peculiar chromosomes thanks to their features, which are puzzling in many ways. They
ignore several commonly accepted biological laws and are escaping the evolutionary
mechanisms of DNA maintenance. Their survival in the population is one of the striking
examples shared with all B chromosomes. Accumulation of B chromosomes via nondisjunction is the most frequently described mechanism with S. purpureosericeum
being not an exception. We observed B-drive during the pollen development at ﬁrst
pollen mitosis. Surprisingly, if this division runs in a regular manner and B-sister
chromatids segregate, the alternative pathway of polymitosis is triggered oﬀ. In thispathway, VCN (carrying B chromosome) is most likely not arrested in the G1 phase but
is allowed to complete the cell cycle and divide again. Right in the frame of this division,
B chromosomes ﬁnally non-disjoin and are passed to a „new“ generative nucleus. This
GCN divides regularly producing two sperms with multiplied B chromosome number.
„Former“ GCN arose from the standard ﬁrst division of unicellular pollen remains
attached to the pollen wall and becomes an extra nucleus.
The work was supported by The Czech Science Foundation (grant no. 22-02108S) andby The Czech Academy of Sciences (project no. DAAD-22-02).

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Plant Chromosome Biology: Cytogenetics meeting 2023

Session 5, Talk, 09:45-10:05

67.
Unveiling Reproductive Diversity: Tree of Sex 2.0 Progress
ReportDr. Sònia Garcia1, Dr. Daniel L. Jeﬀries2, Dr. Cibele G. Sotero-Caio3, Dr. Tatiana Giraud4,
Dr. Paul Jay5, Dr. Lukas Kratochvil6, Dr. Kamil S. Jaron3, Enabling Platforms Team3, Treeof Sex Consortium7
1. Institut Botànic de Barcelona, IBB (CSIC-Ajuntament de Barcelona)
2. Institute for Ecology and Evolution, University of Bern
3. Wellcome Sanger Institute
4. Ecologie Systématique Evolution, CNRS, AgroParisTech, Université Paris-Saclay
5. Center for GeoGenetics, University of Copenhagen
6. Charles University
7. Tree of Sex Consortium
Reproduction is a fundamental aspect of life that has intrigued evolutionary biologists
due to the diverse range of reproductive systems in nature. However, previous research
has primarily focused on a limited number of species, neglecting many aspects ofreproductive diversity. To address this, understanding the full spectrum of reproductive
strategies is crucial for unraveling their connections to life history traits, population
genetics, and genomic and chromosome characteristics.
To achieve this, the Tree of Sex initiative (v2.0, treeofsex.sanger.ac.uk) has beenrelaunched. As an open and highly-collaborative initiative, its aim is to gather
comprehensive information on reproductive systems in eukaryotic life, including sexualand asexual reproduction, the evolution of separate sexes, and the degeneration ofsex/mating-type chromosomes. Over 70 researchers from various institutions anddisciplines have joined this international consortium.
Building upon the original Tree of Sex project, the database incorporates extensive
updates and additional data on relevant reproductive traits. It also integrates genomic
information to keep pace with the expanding ﬁeld and aligns with resources like
Genomes on a Tree (GoaT). Here we discuss the progress made and highlight theevolutionary topics that we aim to explore once the database is populated.

89Plant Chromosome Biology: Cytogenetics meeting 2023

Talk, 10:20-10:40

68.
Plant chromosome biology - Quo vadis?
Andreas Houben1
1. IPK Gatersleben, Germany
In the ﬁeld of plant chromosome biology, signiﬁcant progress has been made based on
the development and application of new technologies. I will discuss how methods likewhole genome sequencing, CRISPR-Cas, chromosome painting, chromosome
engineering and others were used to address fundamental research questions andmight help to advance plant breeding tools.

90Plant Chromosome Biology: Cytogenetics meeting 2023

Session 5, Posters, September 13

Session 5
Specialized chromosomes(Sex chromosomes, B chromosomes and others)

Posters:91

Plant Chromosome Biology: Cytogenetics meeting 2023

Session 5, Posters, September 13

69.
Weird and wonderful – an origin of sex chromosomes in two
races of Rumex hastatulus
Jana Kružlicová1, Václav Bačovský1, Markéta Bodláková1, Stephen Wright2, Roman
Hobza1
1. Department of Plant Developmental Genetics, Institute of Biophysics of the Czech
Academy of Sciences, Kralovopolska 135, 612 65 Brno, Czech Republic
2. Department of Ecology and Evolutionary Biology, University of Toronto, Toronto,
ON, Canada M5S 3B2
Rumex hastatulus is a dioecious plant that evolved into two distinct races with apolymorphic sex chromosome system, XY in Texas (Tx) race and XYY in North Carolina(NC). The time of sex chromosome divergence in the older race (Tx) is estimated to be
9–16 mya, while the younger system (NC) evolved only 0.6 mya. Male plants of Tx race
(2n = 10) possess telocentric X chromosome and large metacentric Y chromosome. In
contrast to Tx race, NC males (2n = 9) underwent a series of chromosomal
rearrangements that led to substantial changes in their genome organization. However,
the exact mechanism through which was NC race genome formed and which parts of
the autosomes were lost has not been completely understood yet. Using the
combination of NGS data and PacBIO technology, we analysed the repeatome of bothraces and identiﬁed sex-speciﬁc satellite candidates for further cytogenetic analysis.
The diﬀerence in the proportion of the sex-speciﬁc satellites and their position revealed
that the neo-sex chromosome system of NC underwent at least two fusions between
the sex chromosomes (X and Y) and one pair of autosomes. These rearrangements were
further accompanied by multiple breakages of the ancestral Y chromosome that led to
the formation of two neo-Y chromosomes (Y1, Y2) in NC males. NC race genome wasfurther shaped by additional inversion and fusion supported by the localization ofsatellites on the autosomes. The exact understanding of the chromosomal
rearrangements that formed the genome of Rumex hastatulus will allow us to study the
epigenetic degeneration of neo-Y chromosomes. Further, this system is an ideal model
to study dosage compensation evolution in old and new sex chromosome systems withthe same evolutionary background and to discover the early mechanisms of sex
chromosome evolution.

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Plant Chromosome Biology: Cytogenetics meeting 2023

Session 5, Posters, September 13

70.
Identiﬁcation of the trans-acting factors that control the nonMendelian drive of the rye B chromosome
Mr Jianyong Chen1, Anastassia Boudichevskaia2, Mark Timothy Rabanus-Wallace1, Anna Voigt1, Zuzana
Tulpova3, Helena Toegelová3, Hana Simkova3, Thomas Schmutzer4, Jiri Macas5, Katharina
Bürstenbinder6, Jan Bartos3, Andreas Houben1
1. Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466 Seeland,
Germany
2. KWS SAAT SE & Co. KGaA, 37574 Einbeck, Germany
3. Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc 77900, Czech
Republic
4. Martin Luther University Halle-Wittenberg, Institute for Agricultural and Nutritional Sciences, 06099
Halle (Saale), Germany
5. Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czech Republic
6. Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Halle (Saale),Germany
The B chromosome (B) is a dispensable element in the genome of many plants, animals, and fungi. To
counteract the elimination of supernumerary chromosomes, many Bs evolved a drive mechanism totransmit themselves at a higher frequency compared to the standard A chromosome. To decipher thechromosome drive process, we have selected the B of rye (Secale cereale) as a model. During the ﬁrst
pollen grain mitosis (PMI), rye B sister chromatids continue to stay cohesive rather than separate, andthen both chromatids preferentially enter the generative nucleus. The drive process of the rye B iscontrolled by the trans-acting B-located non-disjunction control region. Bs lacking the non-disjunction
control region (NCR) undergo normal disjunction at the ﬁrst pollen mitosis and therefore do not drive.
The rye B shows an eﬃcient drive also when it is introduced into wheat.
To narrow down the non-disjunction control region, we compared the repeat composition of the longarm of diﬀerent B variants by ﬂuorescence in situ hybridization (FISH) and identiﬁed a subtelomericregion (~8% of the B) that controls the drive of the rye B. To identify the genetic element(s) that control
the non-disjunction of the rye B, we assembled the rye B sequences using PacBio, Hi-C, Nanopore
sequencing, and optical mapping. In addition, 33 RNA-seq data sets from anthers undergoing PMI of rye
and wheat were generated, including of drive-positive and drive-negative specimens. Diﬀerential
expression analysis identiﬁed that only 16 candidates are up-regulate in all the comparisons between
drive-positive and drive-negative data. PCR-based mapping revealed that 10 of the 16 candidates locate
within the NCR. Their tissue- and stage-speciﬁc expression patterns were tested in RNA-seq data from
7 diﬀerent tissues of wheat with Bs. The drive-associated candidate gene NCR28 shows a PMI-speciﬁcand strong expression. NCR28 is encoded by 13 transcriptionally active copies, and FISH conﬁrmed the
NCR-speciﬁc localization and its multiple copy number. Transient expression of an EYFP-NCR28
construct in Nicotiana benthamiana revealed a microtubule-like pattern in dividing cells. Our results shedlight on the mechanism of chromosome drive in plants. Next, CRISPR-Cas9 will be applied to study
further the function of NCR28 in the process of chromosome drive.
Acknowledgements: We thank the China Scholarship Council (CSC202006850005), Deutsche
Forschungsgemeinschaft (DFG) project HO1779/30-1, European Regional Development Fund (No.
CZ.02.1.01/0.0/0.0/16_019/0000827) and IPK Gatersleben for funding and T. Endo (Japan) for
providing the valuable seeds.

93Plant Chromosome Biology: Cytogenetics meeting 2023

Session 5, Posters, September 13

71.
Identiﬁcation and functional characterization of genes
controlling the process of root-speciﬁc B chromosome
elimination in Aegilops speltoides
Gihwan Kim1, Johannes Thiel1, Jedrzej Jakub Szymanski1, Joerg Fuchs1, MohammadReza Hajirezaei1, Suriya Amutha1, Andreas Houben1
1. Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466 Seeland,
Germany
Genome stability is a crucial feature of eukaryotic organisms since the loss or gain ofeven a single chromosome can signiﬁcantly aﬀect normal development and theorganism as a whole. Nonetheless, some organisms tend to eliminate specialized
chromosomes (such as sex or B chromosomes) either partially or entirely in a certain
stage of development. B chromosomes (Bs) are present in some eukaryotic organisms
exclusively in addition to standard A chromosome complement. Whereas someorganisms carry Bs in every tissue, others do not have Bs in some organs or tissues. The
presence or absence of the B chromosome is variable but also depends on thedevelopmental stage of the organism, e.g., the early stage of embryogenesis. The
elimination of Bs in goat grass Aegilops speltoides, is root-speciﬁc and the elimination
undergoes at the onset of embryogenesis (embryo 6 days after pollination). Aided bytechnical advances in microscopic analysis, genome sequencing, and bioinformatics
analysis, the mechanism behind B chromosome elimination in Ae. speltoides isbeginning to unravel; however, the genes controlling this mechanism remain highly
elusive. In this research, we aim to identify the candidate genes that control the processof root-speciﬁc B chromosome elimination by comparative RNA-seq analysis of thetranscriptome from the tissues undergoing B chromosome elimination compared to theexact same tissue from plants that do not carry B chromosomes. Furthermore, thefunction of candidate genes will be characterized using virus-induced gene silencing(VIGS).

94

Plant Chromosome Biology: Cytogenetics meeting 2023

Session 5, Posters, September 13

72.
Dosage compensation mechanism in plants with evolutionary
young sex chromosomes
Pavla Novotná1, Václav Bačovský1, Aline Muyle2, Andreas Houben3, Katrin Kumke3,
Roman Hobza1
1. Institute of Biophysics of the CAS, Kralovopolska 135, 612 65 Brno, Czech Republic
2. Équipe GEE, CEFE, campus CNRS, 1919, route de Mende, 34293 Montpellier 5,
France3. Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstrasse 3,
Gatersleben 06466, Germany
Some organisms evolved mechanism of dosage compensation (DC) to equalize gene
expression between biological sexes. This process aﬀects either the entire X
chromosomes or may exhibit local and incomplete X chromosome locus speciﬁcderegulation, proceeding gene-by-gene to large chromosomal regions. Despite largeadvances in the ﬁeld of sex chromosome biology, the mechanisms through incomplete
DC evolves remains unclear. In dioecious plant, Silene latifolia, early cytological ﬁndings
suggested that the maternal X chromosome is being upregulated similar as in mammals.
Such evidence was recently supported by transcriptomic expression analysis, showing
incomplete DC mechanism in both sexes. Nevertheless, it is not known, whichmechanisms aﬀect the early stages of DC evolution and what epigenetic processes set
the precise expression balance. Here, we show diﬀerent replication patterns between
Xs in homogametic sex using EdU that incorporates into newly synthesized DNA.
Comparing the XY chromosomes and autosomes, we provide hypothetical model of sex
chromosome replication timing and show late replication of paternal X chromosome parm. We provide a missing link between early and recent transcriptomic evidence, anddiscuss future possibilities how to test DC in relation to diﬀerent ploidy level.

95

Plant Chromosome Biology: Cytogenetics meeting 2023

Session 5, Posters, September 13

73.
Characterization of a maize landraces collection concerning
the B chromosome
Lucie Hloušková1, Kateřina Holušová2, Miroslava Karaﬁátová2, Tereza Bojdová2, Radim
Svačina2, Karol Krak3, Jan Bartoš2
1. Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant
Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech
Republic; Department of Cell Biology and Genetics, Faculty of Science, Palacký
University, Šlechtitelů 27, 779 00 Olomouc, Czech Republic
2. Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant
Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech
Republic
3. Faculty of Environmental Sciences, Czech University of Life Sciences Prague,Kamýcká 129, 165 00, Suchdol, Praha, Czech Republic
B chromosomes are classiﬁed as non-essential genomic components whose
performance is rather atypical. They bring no clear beneﬁt to the host, act as parasitic
and still they persist in populations over the ages. Due to maize agronomical
importance, its B chromosome is pioneering the plant B chromosome biology and is
one of the most thoroughly studied.[1] However, the diversity as well as distributionof the maize B chromosome within wild landraces are pending exploration. Here, wereport on B chromosome distribution across the various maize accessions from theCIMMYT germplasm bank. We designed an eﬀective and reliable pipeline including
presence/absence screening of plant individuals using direct PCR followed by a rapid
method for scoring a number of B chromosomes based on droplet digital PCR. Bchromosome diversity was analysed by combining the cytogenetic approach of
ﬂuorescent in situ hybridization with B-speciﬁc repeats and SNPs identiﬁed insequences of a selected set of 100 lines where the B chromosome was detected. Due
to maize agronomical importance, its chromosome B is thoroughly studied and ispioneering in the plant B chromosome biology.
The work was supported by Ministry of Education, Youth and Sports (award no.
LTT19007) and Czech Science Foundation (award no. 23-04887S).

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Plant Chromosome Biology: Cytogenetics meeting 2023

Session 5, Posters, September 13

74.
Sex-chrome version 2.0: a database of green plant species
with sex chromosomes
Joan Pere Pascual-Díaz1, Bohuslav Janousek2, Susanne S. Renner3, Sònia Garcia1
1. Institut Botànic de Barcelona, IBB (CSIC-Ajuntament de Barcelona)
2. Institute of Biophysics of the Czech Academy of Sciences
3. Department of Biology, Washington University
The majority of plant species are hermaphrodite, bearing male and female reproductive
organs within one ﬂower, while only a small number possess distinct sexes. These
separate sexes can be found either in diﬀerent ﬂowers within the same individual(monoecy) or in diﬀerent ﬂowers within separate individuals (dioecy), although othersystems also exist. Due to their infrequent occurrence and wide taxonomic distribution,
it is believed that sex chromosomes have independently evolved in plants multiple
times. These can exhibit microscopic heteromorphism, as seen in species like Coccinia
grandis, or they can be homomorphic, as observed in Asparagus, Ecballium, and Populus.
In this context, we present the new release of the Sex-chrom database(www.sexchrom.csic.es), a resource containing sex chromosome related information forgreen plants, stemming from papers published from 1919 to March 2022 with data for229 species of dioecious green plants. Among them, 124 species exhibit maleheterogamety (XY), 33 species display female heterogamety (ZW) and 55 species ofbryophytes show haploid-phase sex determination (UV). This resource serves as avaluable tool for anyone seeking knowledge on sex chromosomes in green plants.

97

Plant Chromosome Biology: Cytogenetics meeting 2023

Session 5, Posters, September 1375.
Non canonical bases as possible regulators of sex
chromosomes in the dioecious plant Silene latifolia
Ing. Marcel Hubinsky1, RNDr. Roman Hobza, Ph.D1, Dr. Marta Starczak2, Prof. Dr.
Daniel Gackowski2, Dr. Jose Luis Rodriguez Lorenzo1
1. Department of Plant Developmental Genetics, Institute of Biophysics of the Czech
Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
2. Department of Clinical Biochemistry, Faculty of Pharmacy, Ludwik RydygierCollegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, ul.
Karlowicza 24, PO-85-092, Bydgoszcz, Poland
Enzymatic oxidation products of 5-methylcytosine, known as oxi-mCs, have a broad
range of biological functions in mammals. Accumulating data on plants suggests a rolefor 5-hydroxymethylcytosine (5hmC) in the regulation of transposable elements andassociation with heterochromatic regions. Silene latifolia is a model plant for sex
chromosome evolution. It possesses heteromorphic young sex chromosomes with adegenerating Y chromosome characterized by a size increase due to transposable
element accumulation. A global quantiﬁcation showed high values for 5hmC and 5formylcytosine (5fC) comparable to mammals but no diﬀerences based on sex.
Additionally, the global distribution of oxi-mCs in interphase nuclei showed
colocalization with chromocenters except for 5hmC. The signal distribution of 5hmC
was more uniform with partial enrichment in chromocenter territories, suggesting aeuchromatic/heterochromatic character. On metaphasic chromosomes, the diﬀerences
are observed on the signal distribution between both X sex chromosomes.
Chromosome Xf1 displayed overall enrichment of 5hmC and 5fC regarding thechromosome Xf2. Colocalization showed higher correlation between 5mC and 5fC thanwith 5hmC, which may indicate diﬀerential function for 5hmC and 5fC.
Immunoprecipitation analysis of selected sex-linked genes and sex biased TEs showed
diﬀerential regulation based on a clear sex-dependent clustering rather than a gathering
based on the cytosine modiﬁcations.

98Plant Chromosome Biology: Cytogenetics meeting 2023

Session 5, Posters, September 13

76.
Extended reconstruction of transposable elements in plants
using TE-greedy-nester
Pavel Jedlička1, Ivan Vanát2, Matěj Lexa1,2, Marie Krátká1,3 and Eduard Kejnovský1
1. Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences,
Kralovopolska 135, 61200, Brno, Czech Republic
2. Faculty of Informatics, Masaryk University, 60200 Brno, Czech Republic
3. National Centre for Biomolecular Research, Faculty of Science, Masaryk University,
Kamenice 5, 625 00 Brno, Czech Republic

Transposable elements, including LTR retrotransposons, are mobile genetic elements
constituting remarkable portions of plant genomes and signiﬁcantly contribute to genome
structure, size and regulations. Because of high level of their mutual sequence similarity andnumerous insertion into one another, the correct identiﬁcation of full-length LTR
retrotranposons is a challenging bioinformatic task.
Our software, TE-greedy-nester (Lexa et al., 2020) takes an advantage of greedy
algorithm wich allows to mine increasingly fragmented copies of full-length LTR
retrotranposons. We found this tool to be superior in computation time and full-length element
recovary in highly nested regions. Using TE-greedy-nester we showed that e.g. nesting of LTR
retroelements is not random (Jedlicka et al., 2019); nested elements often have lower LTR
similarity than pre-existing ones (Jedlicka et al., 2020); TEs fragmentation and LTR similarity
diﬀers in (i) low-recombining Y chromosome of dioecious Silene latifolia; and (ii) in monocentricand holocentric chromosomes of closely relative species of Juncaceae family.
Recent challenge is integration of tools for detection of other types of repetitiveelements (e.g., tandem repeats and Miniature Inverted TEs – MITEs). Thererfore we redesigned
the entire codebase to support module implementation. Thereafter, we included two otherdetection tools - Tandem Repeat Finder and MiteFinderII (Benson, 1999 and Hu & Shang, 2018,
respectively); and conducted a few initial testing runs on plant genomic sequences.
References:
Lexa M, Jedlicka P, Vanat I, Cervenansky M, Kejnovsky E. TE-greedy-nester: structure-based
detection of LTR retrotransposons and their nesting. Bioinformatics. 2020 Dec 22;36(20):4991-4999.
doi: 10.1093/bioinformatics/btaa632.
Jedlicka P, Lexa M, Kejnovsky E. What Can Long Terminal Repeats Tell Us About the Age of LTR
Retrotransposons, Gene Conversion and Ectopic Recombination? Front Plant Sci. 2020 May 20;11:644.
doi: 10.3389/fpls.2020.00644.
Benson G. Tandem repeats ﬁnder: a program to analyze DNA sequences. Nucleic Acids Res. 1999
Jan 15;27(2):573-80. doi: 10.1093/nar/27.2.573. PMID: 9862982; PMCID: PMC148217.
Hu J, Zheng Y, Shang X. MiteFinderII: a novel tool to identify miniature inverted-repeat transposable
elements hidden in eukaryotic genomes. BMC Med Genomics. 2018 Nov 20;11(Suppl 5):101. doi:
10.1186/s12920-018-0418-y. PMID: 30453969; PMCID: PMC6245586.
Acknowledgment:This work was supported by the Czech Science Foundation [grant number 21-00580S]

99

Plant Chromosome Biology: Cytogenetics meeting 2023

Session 5, Posters, September 13

78.
Assembly of saltgrass genomes reveals unique genomic
features of a dioecious, perennial, halophytic grass
Kashif Nawaz1, Izamar Olivas Orduna1, Dal-Hoe Koo2, Judith Harrington, Sarah
Eppley3, Jesse Poland1*
1. Center for Desert Agriculture, King Abdullah University of Science and Technology(KAUST), Thuwal, Saudi Arabia
2. Kansas State University, Manhattan, Kansas, USA
3. Portland State University, Portland, Oregon, USA
4. Colorado State University, Fort Collins, Colorado, USA*Corresponding authors. Email: jesse.poland@kaust.edu.sa
The climate crisis in agriculture centers on freshwater scarcity. Understanding halophyte
adaptation for productivity without freshwater oﬀers new opportunities for crop improvement
and neodomestication. Saltgrass (Distichlis spp.) is a unique genus of diecious halophytic C4
grasses, growing in tidal plains and saltmarshes with seawater salinity levels. We present highquality telomere-to-telomere phased genome assemblies of four saltgrass genets, revealing an
allotetraploid species comprising of two syntenic subgenomes of ~300 Mb each. Comparing
genets, we identify a novel chromosome fusion between two subgenomes that leads to genetic
diﬀerentiations of two saltgrass species (D. spicata; 2n=40 and D. stricta; 2n=38). Furthermore,
performing extensive population genetics of several saltgrass populations provides the genetic
diversity linked with geographical distribution. Additionally, we report a repeat-rich B
chromosome (~7 Mb) in two of the genets. Using sex-speciﬁc populations, k-mer analyses, we
identiﬁed genomic location for sex-determination. Saltgrass exhibits high saline resistance,
chromosome fusion, B chromosome, and dioecious traits, making it an appealing candidate forneo-domestication in saline environments, and an ideal model plant to study diverse genomic
features.

100Plant Chromosome Biology: Cytogenetics meeting 2023

September, 11, 13:20-13:40

Partners presentations

101

Plant Chromosome Biology: Cytogenetics meeting 2023

September, 11, 13:20-13:25

77.
Overview of the Cellular Imaging Core Facility (CELLIM) CEITEC MU
Mgr. Petra Kučerová, Ph.D.1, mgr inz. Wojciech Jesionek, Ph.D.1, Mgr. Jakub Pospíšil,Ph.D.1, Mgr. Milan Ešner, Ph.D.1
1. Cellular Imaging Core Facility, CEITEC-MU
CELLIM is the Light Microscopy Core Facility of CEITEC MU. It is part of the
CzechBioImaging research infrastructure funded by the Ministry of Education, Youthand Sports of the Czech Republic. Internationally, it is part of the Advanced Light
Microscopy and Medical Imaging Node Brno CZ - European Research Infrastructure
Consortium EuroBioImaging ERIC. CELLIM provides services in the ﬁeld of lightmicroscopy and oﬀers extensive expertise in sample preparation, image acquisition anddata analysis. We provide access to state of the art instrumentation as well as expertisein sample preparation and data analysis. We have expertise/tools for sample
preparation of various types of biological samples for wideﬁeld/confocal/SIM
microscopy. Advanced techniques we oﬀer include 2D single molecule localisation
microscopy, 3D STORM, TIRF microscopy, spectral separation of ﬂuorochromes andlightsheet microscopy. We also have expertise in expansion microscopy and sample
clearing using various protocols. An integral part of our services is image processing andanalysis - deconvolution, 3D rendering, stitching, object segmentation andmeasurement, etc. using various tools.
Further details about the facility, including contact information, an overview of theequipment, upcoming events and access to the online reservation system can be foundon our website: https://cellim.ceitec.cz/. For the latest news from our site, you can al,so
follow us on our Twitter acount (@Ceitec_CellimCF).

102

Plant Chromosome Biology: Cytogenetics meeting 2023

September 11–13, 2023, Brno

List of Participants
Abramov Dmytro, xabramov@mendelu.cz
Institute of Biophysics of the CAS, v. v. i., Královopolská 135, 612 00, Brno, Czech Republic
An Ruifang, an@ipk-gatersleben.de
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466,
Gatersleben, Germany
Bačovský Václav, xbacovs@ibp.cz
Institute of Biophysics of the CAS, v. v. i., Královopolská 135, 612 00, Brno, Czech Republic
Bartoš Jan, bartos@ueb.cas.cz
Institute of Experimental Botany of the Czech Academy of Sciences, v. v. i., Rozvojová 263, 165
02, Prague 6 – Lysolaje, Czech Republic
Bhadra Sreetama, sreetama.bhadra@idiv.de
German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4,04103, Leipzig Germany
Blavet Nicolas, blavet@ibp.cz
Institute of Biophysics of the CAS, v. v. i., Královopolská 135, 612 00, Brno, Czech RepublicBodláková Markéta, palovska@ibp.cz
Institute of Biophysics of the CAS, v. v. i., Královopolská 135, 612 00, Brno, Czech Republic
Borisjuk Nikolai, nborisjuk@hytc.edu.cn
Huaiyin Normal University, West Changjiang Rd 111, 223300, Huai'an, China
Chen Jianyong, chenj@ipk-gatersleben.de
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466,
Gatersleben, Germany
Cuacos Maria, cuacos@ipk-gatersleben.de
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466,
Gatersleben, GermanyČegan Radim, cegan@ibp.cz
Institute of Biophysics of the CAS, v. v. i., Královopolská 135, 612 00, Brno, Czech RepublicČížková Jana, cizkova@ueb.cas.cz
Institute of Experimental Botany of the Czech Academy of Sciences, v. v. i. , Rozvojová 263,
16502, Praha 6 – Lysolaje, Czech RepublicDoležalová Alžběta, dolezalova@ueb.cas.czÚstav experimentální botaniky, Rozvojová 263, 165 02, Praha 6, Czech Republic

103Plant Chromosome Biology: Cytogenetics meeting 2023

September 11–13, 2023, BrnoDoležel Jaroslav, dolezel@ueb.cas.cz
Institute of Experimental Botany of the Czech Academy of Sciences, v. v. i., Rozvojová 263, 165
02, Prague 6 – Lysolaje, Czech Republic
Fajkus Jiří, fajkus@sci.muni.cz
CEITEC, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
Fajkus Petr, fajkuspe@seznam.cz
CEITEC, Masaryk University, Kamenice 5, 62500, Brno, Czech RepublicFranke Paula, franke.paula.w@gmail.com
University of Silesia in Katowice, Bankowa 12, 40-007, Katowice, Poland
Garcia Sònia, sphaeromeria@gmail.com
Universitat de Barcelona, Av Joan XXIII 27-31, 08028, Barcelona, Spain
Guo Xinyi, xinyi.guo@ceitec.muni.cz
CEITEC, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
Heckmann Stefan, heckmann@ipk-gatersleben.de
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466,
Gatersleben, Germany
Heitkam Tony, tony.heitkam@tu-dresden.de
TU Dresden, Zellescher Weg 20b, 01062, Dresden, Germany
Helia Ondřej, 474529@muni.cz
CEITEC, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
Herklotz Veit, veit.herklotz@senckenberg.de
Senckenberg Museum of Natural History Görlitz, Am Museum 1, 02826, Görlitz, Germany
Hobza Roman, hobza@ibp.cz
Institute of Biophysics of the CAS, v. v. i., Královopolská 135, 612 00, Brno, Czech RepublicHoráková Lucie, lhorakova@ibp.cz
Institute of Biophysics of the CAS, v. v. i., Královopolská 135, 612 00, Brno, Czech Republic
Houben Andreas, houben@ipk-gatersleben.de
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466,
Gatersleben, GermanyHřibová Eva, hribova@ueb.cas.cz
Institute of Experimental Botany of the Czech Academy of Sciences, v. v. i., Rozvojová 263, 165
02, Prague 6 – Lysolaje, Czech Republic
Huang Yile, Yile.Huang@ceitec.muni.cz
CEITEC, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
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September 11–13, 2023, Brno

Hubinský Marcel, mhubinsky@ibp.cz
Institute of Biophysics of the CAS, v. v. i., Královopolská 135, 612 00, Brno, Czech RepublicHudzieczek Vojtěch, hudzieczek@ibp.cz
Institute of Biophysics of the CAS, v. v. i., Královopolská 135, 612 00, Brno, Czech Republic
Ishiguro Sara, 222d401d@cloud.kobe-u.jp
Kobe University, Tsurukabuto 3-11, 657-0051, Nada ward, Kobe, Japan
Ishii Takayoshi, ishii.t@tottori-u.ac.jp
Tottori University, Hamasaka 1390, 6800001, Tottori/Tottori, Japan
Janás Petr, Petr.Janas@ceitec.muni.cz
CEITEC, Masaryk University, Kamenice 5, 62500, Brno, Czech RepublicJaníček Tomáš, tjanicek@ibp.cz
Institute of Biophysics of the CAS, v. v. i., Královopolská 135, 612 00, Brno, Czech Republic
Janoušek Bohuslav, janousek@ibp.cz
Institute of Biophysics of the CAS, v. v. i., Královopolská 135, 612 00, Brno, Czech Republic
Jedlička Pavel, jedlicka@ibp.cz
Institute of Biophysics of the CAS, v. v. i., Královopolská 135, 612 00, Brno, Czech Republic
Jesionek Wojciech, wojciech.jesionek@ceitec.muni.cz
CEITEC, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
Jiang Hua, jiangh@ipk-gatersleben.de
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466,
Gatersleben, Germany
Kajan Grodecká Lucie, grodecka.l@ibp.cz
Institute of Biophysics of the CAS, v. v. i., Královopolská 135, 612 00, Brno, Czech Republic
Karaﬁátová Miroslava, karaﬁatova@ueb.cas.cz
Institute of Experimental Botany of the Czech Academy of Sciences, v. v. i., Rozvojová 263, 165
02, Prague 6 – Lysolaje, Czech Republic
Kejnovský Eduard, kejnovsk@ibp.cz
Institute of Biophysics of the CAS, v. v. i., Královopolská 135, 612 00, Brno, Czech Republic
Khosravi Solmaz, khosravi@ipk-gatersleben.de
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466,
Gatersleben, Germany
Kim Gihwan, kimg@ipk-gatersleben.de
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466,
Gatersleben, Germany
105

Plant Chromosome Biology: Cytogenetics meeting 2023

September 11–13, 2023, Brno

Koláčková Veronika, kolackova@ueb.cas.cz
Institute of Experimental Botany of the Czech Academy of Sciences, v. v. i., Rozvojová 263, 165
02, Prague 6 – Lysolaje, Czech Republic
Kolano Bożena, bozena.kolano@us.edu.pl
University of Silesia in Katowice, Bankowa 12, 40-007, Katowice, Poland
Krátká Marie, kratka@ibp.cz
Institute of Biophysics of the CAS, v. v. i., Královopolská 135, 612 00, Brno, Czech RepublicKružlicová Jana, janka.kruzlicova@gmail.com
Institute of Biophysics of the CAS, v. v. i., Královopolská 135, 612 00, Brno, Czech Republic
Kubát Zdeněk, kubat@ibp.cz
Institute of Biophysics of the CAS, v. v. i., Královopolská 135, 612 00, Brno, Czech Republic
Kučerová Petra, petra.kucerova@ceitec.muni.cz
CEITEC, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
Kuo Yi-Tzu, kuo@ipk-gatersleben.de
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466,
Gatersleben, Germany
Lermontova Inna, lermonto@ipk-gatersleben.de
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466,
Gatersleben, Germany
Lexa Matej, lexa@ibp.cz
Institute of Biophysics of the CAS, v. v. i., Královopolská 135, 612 00, Brno, Czech Republic
Lunerová Jana, jana.luner@ibp.cz
Institute of Biophysics of the CAS, v. v. i., Královopolská 135, 612 00, Brno, Czech Republic
Lysák Martin, martin.lysak@ceitec.muni.cz
CEITEC, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
Lyu Zhenling, zlyu@uni-bonn.de,
Bonn University, Kirschallee 1, 53115, Bonn, Germany
Ma YIngrui, may@ipk-gatersleben.de
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466,
Gatersleben, Germany
Macas Jiří, macas@umbr.cas.cz
Biology Centre of the CAS, Branišovská 31, 37005, České Budějovice, Czech RepublicMachálková Zuzana, zmachalkova@ibp.cz
Institute of Biophysics of the CAS, v. v. i., Královopolská 135, 612 00, Brno, Czech Republic
106Plant Chromosome Biology: Cytogenetics meeting 2023

September 11–13, 2023, Brno

Maiwald Sophie, Sophie.Maiwald@tu-dresden.de
TU Dresden, Zellescher Weg 20b, 01217, Dresden, Germany
Mandáková Terezie, terezie.mandakova@ceitec.muni.cz
CEITEC, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
Mann Ludwig, ludwig.mann@tu-dresden.de
TU Dresden, Zellescher Weg 20b, 01217, Dresden, Germany
Martin Azahara C., azahara.martin@ias.csic.es
Institute for Sustainable Agriculture (IAS-CSIC), Campus Alameda del Obispo s/n, 14004,
Córdoba, Spain
Mašek Jan, masek@ibp.cz
Institute of Biophysics of the CAS, v. v. i., Královopolská 135, 612 00, Brno, Czech RepublicMolnár István, molnar.istvan@atk.hu
Centre for Agricultural Research, Brunszvik 2., H-2462, Martonvásár, Hungary
Mykhailyk Serhii, serhii.mykhailyk@us.edu.pl
Uniwersytet Śląski, ul. Bankowa 12, 40-007, Katowice, Polska
Nascimento Thiago, thiagoagtc@gmail.com
Max-Planck Institute of Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Köln,
Germany
Nawaz Kashif, kashif.nawaz@kaust.edu.sa
King Abdullah University of Science and Technology, 23955, Thuwal, Saudi Arabia
Nešpor Dadejová Martina, nespor.dadejova@centrum.cz
CEITEC, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
Neumann Pavel, neumann@umbr.cas.cz
Biology Centre of the CAS, Branišovská 31, 37005, České Budějovice, Czech RepublicNovák Petr, petr@umbr.cas.cz
Biology Centre of the CAS, Branišovská 31, 37005, České Budějovice, Czech Republic
Novotná Pavla, novotna@ibp.cz
Institute of Biophysics of the CAS, v. v. i., Královopolská 135, 612 00, Brno, Czech Republic
Nowicka Anna , nowicka@ueb.cas.cz
Institute of Experimental Botany of the Czech Academy of Sciences, v. v. i., Rozvojová 263, 165
02, Prague 6 – Lysolaje, Czech Republic
Ohmido Nobuko, ohmido@kobe-u.ac.jp
Graduate School of Human Development and Environment, Kobe University, Tsurukabuto 311, 657-8501, Nada, Kobe, Japan107

Plant Chromosome Biology: Cytogenetics meeting 2023

September 11–13, 2023, Brno

Okamoto Takashi, okamoto-takashi@tmu.ac.jp
Tokyo Metropolitan University, Minami-osawa 1-1, 192-0397, Hachioji, Tokyo, Japan
Oliveira Ludmila, lud.oliveira@gmail.com
Biology Centre of the CAS, Branišovská 31, 37005, České Budějovice, Czech Republic
Ono Eiichiro, Eiichiro_Ono@suntory.co.jp
Suntory Global Innovatoin Center Ltd., 8-1-1 Seikadai, Seika, Soraku, 619-0284 Kyoto, Japan
Pascual-Díaz Joan Pere, joanpere.pascual@ibb.csic.es
Universitat de Barcelona, AV JOAN XXIII 27-31, 08028, Barcelona, Spain
Pečinka Aleš, pecinka@ueb.cas.cz
The Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31, 77900,
Olomouc, Czech Republic
Potlapalli Bhanu Prakash, potlapalli@ipk-gatersleben.de
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466,
Gatersleben, Germany
Pouch Milan, milan.pouch@ceitec.muni.cz
CEITEC, Masaryk University, Kamenice 5, 62500, Brno, Czech RepublicPuchta Holger, holger.puchta@kit.edu
Joseph Gottlieb Kölreuter Institute for Plant Sciences, Karlsruhe Institute of Technology (KIT),
Fritz-Haber-Weg 4 Geb. 30.43, D-76133, Karlsruhe, Germany
Quirós de la Peña Begoña, bego8estudiante@gmail.com
Charles University, Albertov 6, 128 00, Praha 2, Czech Republic
Rahmatov Mahbubjon, mahbubjon.rahmatov@slu.se
Swedish University of Agricultural Sciences, Sundvvagen 10, 23053, Alnarp, Sweden
Ritz Christiane , christiane.ritz@senckenberg.de
Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325, Frankfurt,
Germany
Rodríguez Jose Luis, rodriguez@ibp.cz
Institute of Biophysics of the CAS, v. v. i., Královopolská 135, 612 00, Brno, Czech Republic
Said Mahmoud, said@ueb.cas.cz
Institute of Experimental Botany of the Czech Academy of Sciences, v. v. i., Rozvojová 263, 165
02, Prague 6 – Lysolaje, Czech Republic
Severyns Astrid Johanna Irena, astrid.severyns@kuleuven.be
Plant Genetics and Crop Improvement lab (KU Leuven), Celestijnenlaan 43, 0101, 3001,
Heverlee, Belgium

108Plant Chromosome Biology: Cytogenetics meeting 2023

September 11–13, 2023, Brno

Shahbazi Mehrdad, shahbazi@ueb.cas.cz
Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31, 77900,
Olomouc, Czech Republic
Shimomai Hina, 220d408d@gsuite.kobe-u.ac.jp
Kobe University, Tsurukabuto 3-11, 6570011, Kobe city, Nada ward, Japan
Schmidt Nicola, nicola.schmidt@tu-dresden.de
TU Dresden, Zellescher Weg 20b, 01217, Dresden, Germany
Schneeweiss Hanna, hanna.schneeweiss@univie.ac.atUniversity of Vienna, Rennweg 14, 1030, Vienna, Austria
Schubert Ingo, schubert@ipk-gatersleben.de
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466,
Gatersleben, Germany
Schwarzacher Trude, ts32@le.ac.uk
University of Leicester, University Road, LE1 7RH, Leicester, UK
Steckenborn Stefan, ssteckenborn@mpipz.mpg.de
Max-Planck-Institut für Pﬂanzenzüchtungsforschung, Carl-von-Linné-Weg 10, 50829, Köln,
Germany
Strejčková Beáta, strejckova@ueb.cas.cz
Institute of Experimental Botany of the Czech Academy of Sciences, v. v. i., Rozvojová 263, 165
02, Prague 6 – Lysolaje, Czech RepublicSýkorová Eva, evin@ibp.cz
Institute of Biophysics of the CAS, v. v. i., Královopolská 135, 612 00, Brno, Czech Republic
Szecówka Jana, szecowkaj@ueb.cas.cz
The Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31, 77900,
Olomouc, Czech RepublicŠafář Jan, safar@ueb.cas.cz
Institute of Experimental Botany of the Czech Academy of Sciences, v. v. i., Rozvojová 263, 165
02, Prague 6 – Lysolaje, Czech RepublicŠimková Hana, SimkovaH@ueb.cas.cz
Institute of Experimental Botany of the Czech Academy of Sciences, v. v. i., Rozvojová 263, 165
02, Prague 6 – Lysolaje, Czech RepublicŠlajsová Tereza, vojtkova@ueb.cas.cz
Institute of Experimental Botany of the Czech Academy of Sciences, v. v. i., Rozvojová 263, 165
02, Prague 6 – Lysolaje, Czech Republic

109Plant Chromosome Biology: Cytogenetics meeting 2023

September 11–13, 2023, Brno

Tamilselvan Nattar Amutha Suriya, amutha@ipk-gatersleben.de
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466,
Gatersleben, Germany
Tokan Viktor, viktor.tokan@ibp.cz
Institute of Biophysics of the CAS, v. v. i., Královopolská 135, 612 00, Brno, Czech Republic
Trunova Dana, dana.trunova@us.edu.pl
University of Silesia in Katowice, Bankowa 12, 40007, Katowice, Poland
Vozárová Radka, vozarova@ibp.cz
Institute of Biophysics of the CAS, v. v. i., Královopolská 135, 612 00, Brno, Czech Republic
Vyskot Boris, vyskot@ibp.cz
Institute of Biophysics of the CAS, v. v. i., Královopolská 135, 612 00, Brno, Czech Republic
Waminal Nomar, waminal@ipk-gatersleben.de
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466,
Gatersleben, Germany
Wang Baicui, wangb@ipk-gatersleben.de
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466,
Gatersleben, Germany
Yadala Ramakrishna, yadala@ipk-gatersleben.de
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466,
Gatersleben, Germany
Zheng Shiwei, zheng@ipk-gatersleben.de
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466,
Gatersleben, Germany
Zhou Sida, zhous@ipk-gatersleben.de
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466,
Gatersleben, Germany

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Plant Chromosome Biology: Cytogenetics meeting 2023

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Plant Chromosome Biology: Cytogenetics meeting 2023

September 11–13, 2023, Brno

Plant Chromosome Biology: Cytogenetics meeting 2023

September 11–13, 2023, Brno