# Sequencing, annotation, and pangenomics in wheat

Frédéric Choulet

► To cite this version:

Frédéric Choulet. Sequencing, annotation, and pangenomics in wheat. Webinaire de l'AFBV, Association Française des Biotechnologies Végétales, May 2022, Clermont-Ferrand, France. hal-04090082

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<figure><img src="image_1.png" /></figure>

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# Sequencing, annotation, and
pangenomics in wheat

Frédéric Choulet

GDEC, Clermont-Ferrand, France

<figure><img src="image_2.png" /></figure>

Genetics Diversity Ecophysiology of Cereals

<figure><img src="image_3.png" /></figure>

UNIVERSITÉ
Clermont
Auvergne

<figure><img src="image_4.png" /></figure>
# 1. Introduction

- Wheat/Triticeae

- Pangenomics
Genome size

<figure><img src="image_5.png" /></figure>

Poaceae

Sorghum

Maize

Rice

Brachypodium

Barley

Wheat

Triticeae
Triticeae

<figure><img src="image_6.png" /></figure>

HH

Hordeum

<figure><img src="image_7.png" /></figure>

AA

Triticum urartu

DD

Aegilops tauschii

AABBDD

Triticum aestivum

AABB

Triticum durum

BB

Aegilops speltoides

<figure><img src="image_8.png" /></figure>

<figure><img src="image_9.png" /></figure>

<figure><img src="image_10.png" /></figure>
<figure><img src="image_11.png" /></figure>

## Complex genome

* 15 Gb

* Hexaploid AA-BB-DD

* 85% TEs

* Ref cultivar: Chinese Spring

<figure><img src="image_12.png" /></figure>

## Assembly (v1)

* 21 chromosomes (14.5 Gb)

## Annotation (v1.1)

* 107k genes

* 4 million TEs

<figure><img src="image_13.png" /></figure>
<figure><img src="image_14.png" /></figure>

~1 Mb
○ RQAs: Reference-Quality Assemblies of *Triticeae* genomes

<figure><img src="image_15.png" /></figure>

Li et al., Mol Plant 2022

► *T. aestivum*:
Chinese Spring + 17 accessions
o SNP genotyping of 4500 accessions representing world-wide diversity

<figure><img src="image_16.png" /></figure>
○ Pangenomics

<figure><img src="image_17.png" /></figure>

Tettelin et al. PNAS 2005

8 genomes of *S. agalactiae*

<figure><img src="image_18.png" /></figure>

<figure><img src="image_19.png" /></figure>

<figure><img src="image_20.png" /></figure>
o Structural Variations (SVs)

<figure><img src="image_21.png" /></figure>
➤ Koonin and Wolf NAR 2008
bacteria, archea (~700 genomes)

<figure><img src="image_22.png" /></figure>

<figure><img src="image_23.png" /></figure>
## ○ Pangenomics in plants

*De novo* assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits

Ying-hui Li¹⁻³,¹¹, Guangyu Zhou⁴,¹⁰,¹¹, Jianxin Ma⁵,¹¹, Wenkai Jiang⁴,¹¹, Long-guo Jin¹⁻³, Zhouhao Zhang⁴,
Yong Guo¹⁻³, Jinbo Zhang⁴, Yi Sui¹⁻³, Liangtao Zheng⁴, Shan-shan Zhang¹⁻³, Qiyang Zuo⁴, Xue-hui Shi¹⁻³,
Yan-fei Li¹⁻³, Wan-ke Zhang⁶, Yiyao Hu⁴, Guanyi Kong⁴, Hui-long Hong¹⁻³, Bing Tan¹⁻³, Jian Song¹⁻³,
Zhang-xiong Liu¹⁻³, Yaoshen Wang⁴, Hang Ruan⁴, Carol K L Yeung⁴, Jian Liu⁴, Hailong Wang⁴, Li-juan Zhang¹⁻³,
Rong-xia Guan¹⁻³, Ke-jing Wang¹⁻³, Wen-bin Li⁷, Shou-yi Chen⁶, Ru-zhen Chang¹⁻³, Zhi Jiang⁴,
Scott A Jackson⁸, Ruiqiang Li⁴,⁹ & Li-juan Qiu¹⁻³

NATURE BIOTECHNOLOGY VOLUME 32 NUMBER 10 OCTOBER 2014

7 genomes of *Glycine soja*
dispensable: ~20% genes

Extensive gene content variation in the
*Brachypodium distachyon* pan-genome correlates
with population structure

Sean P. Gordon¹, Bruno Contreras-Moreira ◦ 2,3,4, Daniel P. Woods⁵,⁶, David L. Des Marais ◦ 7,17, Diane Burgess⁸, Shengqiang Shu¹, Christoph Stritt⁹, Anne C. Roulin⁹, Wendy Schackwitz¹, Ludmila Tyler¹⁰, Joel Martin ◦ 1, Anna Lipzen¹, Niklas Dochy ◦ 11, Jeremy Phillips¹, Kerrie Barry¹, Koen Geuten ◦ 11, Hikmet Budak ◦ 12, Thomas E. Juenger¹³, Richard Amasino ◦ 5,6, Ana L. Caicedo ◦ 10, David Goodstein ◦ 1, Patrick Davidson¹, Luis A. J. Mur ◦ 14, Melanie Figueroa ◦ 15, Michael Freeling⁸, Pilar Catalan ◦ 4,16 & John P. Vogel ◦ 1,8

NATURE COMMUNICATIONS | 8:2184 | DOI: 10.1038/s41467-017-02292-8 | www.nature.com/naturecommunications 2017

54 genomes of *Brachypodium distachyon*

<figure><img src="image_24.png" /></figure>

<figure><img src="image_25.png" /></figure>

27% (dispensable)

73% (core)

<figure><img src="image_26.png" /></figure>

34%

<figure><img src="image_27.png" /></figure>
## ○ Pangenomics in plants

### The pangenome of an agronomically important
crop plant *Brassica oleracea*

Agnieszka A. Golicz¹, Philipp E. Bayer², Guy C. Barker³, Patrick P. Edger⁴, HyeRan Kim⁵, Paula A. Martinez¹, Chon Kit Kenneth Chan², Anita Severn-Ellis², W. Richard McCombie⁶, Isobel A.P. Parkin⁷, Andrew H. Paterson⁸, J. Chris Pires⁹, Andrew G. Sharpe¹⁰, Haibao Tang¹¹, Graham R. Teakle³, Christopher D. Town¹², Jacqueline Batley² & David Edwards²

NATURE COMMUNICATIONS | 7:13390 | DOI: 10.1038/ncomms13390 | www.nature.com/naturecommunications 2016

9 genomes of *Brassica oleracea*
dispensable: ~20% genes

### Pan-genome analysis highlights the extent of
genomic variation in cultivated and wild rice

Qiang Zhao¹, Qi Feng¹, Hengyun Lu¹, Yan Li¹, Ahong Wang¹, Qilin Tian¹, Qilin Zhan¹, Yiqi Lu¹, Lei Zhang¹, Tao Huang¹, Yongchun Wang¹, Danlin Fan¹, Yan Zhao¹, Ziqun Wang¹, Congcong Zhou¹, Jiaying Chen¹, Chuanrang Zhu¹, Wenjun Li¹, Qijun Weng¹, Qun Xu², Zi-Xuan Wang¹, Xinghua Wei², Bin Han¹ and Xuehui Huang¹,³*

NATURE GENETICS | VOL 50 | FEBRUARY 2018 | 278-284 | www.nature.com/naturegenetics

67 genomes of *Oryza sativa* + *rufipogon*
~20% genes

<figure><img src="image_28.png" /></figure>
## o Pangenomics in plants

The Plant Cell, Vol. 26: 121-135, January 2014, www.plantcell.org © 2014.

**Insights into the Maize Pan-Genome and Pan-Transcriptome**
WIOPEN

Candice N. Hirsch,ª,ᵇ,¹ Jillian M. Foerster,ᶜ,² James M. Johnson,ᶜ,³ Rajandeep S. Sekhon,ᶜ,ᵈ German Muttoni,ᶜ,⁴

Brieanne Vaillancourt,ª,ᵇ Francisco Peñagaricano,ᵉ Erika Lindquist,¹ Mary Ann Pedraza,¹ Kerrie Barry,¹

Natalia de Leon,ᶜ,ᵈ Shawn M. Kaeppler,ᶜ,ᵈ and C. Robin Buellª,ᵇ,⁵

503 maize accessions (RNAseq)
=> ~8700 novel transcripts

Darracq et al. BMC Genomics (2018) 19:119

DOI 10.1186/s12864-018-4490-7

<figure><img src="image_29.png" /></figure>

CrossMark

**Sequence analysis of European maize inbred line F2 provides new insights into molecular and chromosomal characteristics of presence/absence variants**

Aude Darracq¹†, Clémentine Vitte¹†, Stéphane Nicolas¹, Jorge Duarte², Jean-Philippe Pichon², Tristan Mary-Huard¹,³, Céline Chevalier¹, Aurélie Bérard⁴, Marie-Christine Le Paslier⁴, Peter Rogowsky⁵, Alain Charcosset¹ and Johann Joets¹*

### Dispensable vs core genes:

- shorter, fewer introns

- less expressed, fewer conditions

- evolve more rapidly

- enriched in functions related to adaptation, response to env
## ○ Pangenomics in plants

### High-resolution genetic mapping of maize pan-genome sequence anchors

Fei Lu¹, Maria C. Romay¹, Jeffrey C. Glaubitz¹, Peter J. Bradbury², Robert J. Elshire¹, Tianyu Wang³, Yu Li³, Yongxiang Li³, Kassa Semagn⁴, Xuecai Zhang⁵, Alvaro G. Hernandez⁶, Mark A. Mikel⁶,⁷, Ilya Soifer⁸, Omer Barad⁸ & Edward S. Buckler¹,²

NATURE COMMUNICATIONS | 6:6914 | DOI: 10.1038/ncomms7914 | www.nature.com/naturecommunications 2015

> "PAV SNPs exhibit enriched associations with traits"

<figure><img src="image_30.png" /><figcaption>b</figcaption></figure>

<figure><img src="image_31.png" /><figcaption>c</figcaption></figure>

<figure><img src="image_32.png" /><figcaption>d</figcaption></figure>

<figure><img src="image_33.png" /></figure>
o Pangenomics in plants

The tomato pan-genome uncovers new genes and
a rare allele regulating fruit flavor

Lei Gao<sup>1,10</sup>, Itay Gonda<sup>1,2,10</sup>, Honghe Sun<sup>1</sup>, Qiyue Ma<sup>1</sup>, Kan Bao<sup>1</sup>, Denise M. Tieman<sup>3</sup>, Elizabeth A. Burzynski-Chang<sup>4</sup>, Tara L. Fish<sup>5</sup>, Kaitlin A. Stromberg<sup>1</sup>, Gavin L. Sacks<sup>6</sup>, Theodore W. Thannhauser<sup>5</sup>, Majid R. Foolad<sup>6</sup>, Maria Jose Diez<sup>7</sup>, Jose Blanca<sup>7</sup>, Joaquin Canizares<sup>7</sup>, Yimin Xu<sup>1</sup>, Esther van der Knaap<sup>8</sup>, Sanwen Huang<sup>9</sup>, Harry J. Klee<sup>3</sup>, James J. Giovannoni<sup>1,5*</sup> and Zhangjun Fei<sup>1,5*</sup>

NATURE GENETICS | VOL 51 | JUNE 2019 | 1044-1051 | www.nature.com/naturegenetics

725 genomes of *Solanum* cultivated + 3 wild species core: **74%** genes

"The most striking feature of the tomato pan-genome was its **high core** gene content (74.2%), as compared with those of *Arabidopsis thaliana* (70%), *Brassica napus* (62%), *bread wheat* (64%), *rice* (54%), wild *soybean* (49%) and *Brachypodium distachyon* (35%)"
o Pangenomics in plants

The pangenome of hexaploid bread wheat

Juan D. Montenegro<sup>1,†</sup>, Agnieszka A. Golicz<sup>1,2,†,‡</sup>, Philipp E. Bayer<sup>2,†</sup>, Bhavna Hurgobin<sup>1,2</sup>, HueyTyng Lee<sup>1,2</sup>, Chon-Kit Kenneth Chan<sup>2</sup>, Paul Visendi<sup>1</sup>, Kaitao Lai<sup>3</sup>, Jaroslav Doležel<sup>4</sup>, Jacqueline Batley<sup>1,2,5</sup> and David Edwards<sup>1,2,5,*</sup>

*The Plant Journal* (2017) **90**, 1007–1013

16 Australian wheat cultivars (Illumina reseq)
dispensable: ~35% of genes

15 wheat genomes assembled

* "12% of genes showed PAVs"

* "26% of the projected genes were found in tandem duplications, indicating that CNV is a strong contributor of genetic variation in wheat"

Multiple wheat genomes reveal global
variation in modern breeding

https://doi.org/10.1038/s41586-020-2961-x

Sean Walkowiak<sup>1,4,†</sup>, Liangliang Gao<sup>3,4,†</sup>, Cecile Monat<sup>4,4†</sup>, Georg Haberer<sup>5</sup>, Mulualem T. Kassa<sup>4</sup>, Jemima Brinton<sup>7</sup>, Ricardo H. Ramirez-Gonzalez<sup>7</sup>, Markus C. Kolodziej<sup>7</sup>, Emily Delorean<sup>8</sup>, Dinushika Thambugala<sup>9</sup>, Valentyna Klymiuk<sup>1</sup>, Brook Byrns<sup>1</sup>, Heidrun Gundlach<sup>10</sup>, Venkat Bandi<sup>10</sup>, Jorge Nunez Siri<sup>10</sup>, Kirby Nilsen<sup>11</sup>, Catharine Aquino<sup>12</sup>, Axel Himmelbach<sup>4</sup>, Dario Copetti<sup>13,4</sup>, Tomohiro Ban<sup>5</sup>, Luca Venturini<sup>16</sup>, Michael Bevan<sup>1</sup>, Bernardo Clavijo<sup>17</sup>, Dal-Hoe Koo<sup>3</sup>, Jennifer Ens<sup>1</sup>, Krystalee Wiebe<sup>1</sup>, Amidou N'Diaye<sup>1</sup>, Allen K. Fritz<sup>2</sup>, Carl Gutwin<sup>10</sup>, Anne Fiebig<sup>4</sup>, Christine Fosker<sup>11</sup>, Bin Xiao Fu<sup>2</sup>, Gonzalo Garcia Accinelli<sup>17</sup>, Keith A. Gardner<sup>18</sup>, Nick Fradgley<sup>18</sup>, Juan Gutierrez-Gonzalez<sup>19</sup>, Gwyneth Halstead-Nussloch<sup>13</sup>, Masaomi Hatakeyama<sup>12,13</sup>, Chu Shin Koh<sup>20</sup>, Jasline Deek<sup>21</sup>, Alejandro C. Costamagna<sup>22</sup>, Pierre Fobert<sup>6</sup>, Darren Heavens<sup>17</sup>, Hiroyuki Kanamori<sup>23</sup>, Kanako Kawaura<sup>15</sup>, Fuminori Kobayashi<sup>23</sup>, Ksenia Krasileva<sup>17</sup>, Tony Kuo<sup>24,25</sup>, Neil McKenzie<sup>1</sup>, Kazuki Murata<sup>26</sup>, Yusuke Nabeka<sup>28</sup>, Timothy Paape<sup>13</sup>, Sudharsan Padmarasu<sup>5</sup>, Lawrence Percival-Alwyn<sup>18</sup>, Sateesh Kagale<sup>6</sup>, Uwe Solz<sup>4</sup>, Jun Sese<sup>26,27</sup>, Philomin Juliana<sup>28</sup>, Ravi Singh<sup>28</sup>, Rie Shimizu-Intsugi<sup>15</sup>, David Swarbreck<sup>17</sup>, James Cockram<sup>18</sup>, Hikmet Budak<sup>29</sup>, Toshiaki Tameshige<sup>16</sup>, Tsuyoshi Tanaka<sup>23</sup>, Hiroyuki Tsuji<sup>15</sup>, Jonathan Wright<sup>17</sup>, Jianzhong Wu<sup>23</sup>, Burkhard Steuernagel<sup>7</sup>, Ian Small<sup>30</sup>, Sylvie Cloutier<sup>31</sup>, Gabriel Keeble-Gagnère<sup>22</sup>, Gary Muehlbauer<sup>19</sup>, Josquin Tibbets<sup>22</sup>, Shuhei Nasuda<sup>26</sup>, Joanna Melonek<sup>30</sup>, Pierre J. Hucl<sup>1</sup>, Andrew G. Sharpe<sup>20</sup>, Matthew Clark<sup>16</sup>, Erik Legg<sup>33</sup>, Arvind Bharti<sup>33</sup>, Peter Langridge<sup>34</sup>, Anthony Hall<sup>17</sup>, Cristobal Uauy<sup>7</sup>, Martin Mascher<sup>4,35</sup>, Simon G. Krattinger<sup>8,36</sup>, Hirokazu Handa<sup>23,27</sup>, Kentaro K. Shimizu<sup>15,15</sup>, Assaf Distelfeld<sup>28</sup>, Ken Chalmers<sup>34</sup>, Beat Keller<sup>8</sup>, Klaus F. X. Mayer<sup>3,39</sup>, Jesse Poland<sup>3</sup>, Nils Stein<sup>4,40</sup>, Curt A. McCartney<sup>9,52</sup>, Manuel Spannagl<sup>5,53</sup>, Thomas Wicker<sup>2,53</sup> & Curtis J. Pozniak<sup>130</sup>

<figure><img src="image_34.png" /></figure>
○ Build and visualize pangenomes

<figure><img src="image_35.png" /></figure>

<figure><img src="image_36.png" /></figure>

GenomicusPlants — database version: 49.01 / Web-code version: 2021-08-15 — Dyogen Team
<figure><img src="image_37.png" /></figure>

pangenome graph of
~3000 Acinetobacter

PPanGGOLiN

<figure><img src="image_38.png" /></figure>
## Practical Haplotype Graph

A sorghum practical haplotype graph facilitates genome-wide imputation and cost-effective genomic prediction

Sarah E. Jensen¹ ⚙️ | Jean Rigaud Charles² ⚙️ | Kebede Muleta³ ⚙️ |

Peter J. Bradbury⁴,⁶ ⚙️ | Terry Casstevens⁴ ⚙️ | Santosh P. Deshpande⁵ ⚙️ |

Michael A. Gore¹ ⚙️ | Rajeev Gupta⁵ ⚙️ | Daniel C. Ilut¹ ⚙️ | Lynn Johnson⁴ ⚙️ |

Roberto Lozano¹ ⚙️ | Zachary Miller⁴ ⚙️ | Punna Ramu⁴ ⚙️ | Abhishek Rathore⁵ ⚙️ |

M. Cinta Romay⁴ ⚙️ | Hari D. Upadhyaya⁵ ⚙️ | Rajeev K. Varshney⁵ ⚙️ |

Geoffrey P. Morris³ ⚙️ | Gael Pressoir² ⚙️ | Edward S. Buckler¹,⁴,⁶ ⚙️ |

Guillaume P. Ramstein⁴ ⚙️

Plant Genome, 2020;13:e20009.
https://doi.org/10.1002/tpg2.20009

* for breeding programs

* based on a limited number of founder lines

* 0.01x skim-seq ->call SNPs with 5% errors

<figure><img src="image_39.png" /></figure>

Development of the Wheat Practical Haplotype Graph
database as a resource for genotyping data storage and
genotype imputation

Katherine W. Jordan ID, ¹,²,† Peter J. Bradbury ID, ³ Zachary R. Miller,⁴ Moses Nyine ID, ¹ Fei He,¹ Max Fraser,⁵ Jim Anderson,⁵

Esten Mason,⁶ Andrew Katz,⁶ Stephen Pearce ID,⁶ Arron H. Carter,⁷ Samuel Prather,⁷ Michael Pumphrey,⁷ Jianli Chen,⁸

Jason Cook,⁹ Shuyu Liu,¹⁰ Jackie C. Rudd,¹⁰ Zhen Wang,¹⁰ Chenggen Chu ID,¹⁰ Amir M. H. Ibrahim,¹⁰ Jonathan Turkus,¹¹

Eric Olson,¹¹ Ragupathi Nagarajan,¹² Brett Carver,¹² Liuling Yan,¹² Ellie Taagen,⁴ Mark Sorrells,⁴ Brian Ward,¹³ Jie Ren,¹,¹⁴

Alina Akhunova,¹,¹⁴ Guihua Bai,² Robert Bowden,² Jason Fiedler,¹⁵ Justin Faris ID,¹⁵ Jorge Dubcovsky ID,¹⁶ Mary Guttieri,²

Gina Brown-Guedira,¹³ Ed Buckler,³ Jean-Luc Jannink ID,³ and Eduard D. Akhunov ID ¹,*

G3, 2022, 12(2), jkab390

* 65 wheat lines, exome capture

* 0.01x -> imputations with 8% errors
2. Wheat genome sequencing, annotation, A-B-D comparative genomics

Shifting the limits in wheat research
and breeding using a fully annotated
reference genome

International Wheat Genome Sequencing Consortium (IWGSC)*
o Predicting genes is still NOT routine

**GDEC** Clermont, France – *Rimbert Leroy Choulet et al.*

**PGSB** Munich, Germany – *Spannagl Twardziok et al.*

**EI** Norwich, UK – *Swarbreck Venturini et al.*

<figure><img src="image_40.png" /></figure>

IWGSC RefSeq (Chinese Spring)

• 107,891 genes

<figure><img src="image_41.png" /></figure>
HighConfidenceGenesv1.1 (GOMAP annotation available)

Sorghum bicolor

Hordeum vulgare var. distichum

Aegilops tauschii

Triticum urartu

Brachypodium distachyon

Oryza barthii

Zea mays

Triticum aestivum RNA-Seq (Pingault et al. 2014)

<figure><img src="image_42.png" /></figure>
* HighConfidenceGenesv1.1 (GOMAP annotation available)

<figure><img src="image_43.png" /></figure>

<figure><img src="image_44.png" /></figure>

* Sorghum bicolor

<figure><img src="image_45.png" /></figure>

* Hordeum vulgare var. distichum

<figure><img src="image_46.png" /></figure>

* Aegilops tauschii

* Triticum urartu

* Brachypodium distachyon

<figure><img src="image_47.png" /></figure>

* Oryza barthii

<figure><img src="image_48.png" /></figure>

* Zea mays

<figure><img src="image_49.png" /></figure>

* Triticum aestivum RNA-Seq (Pingault et al. 2014)

<figure><img src="image_50.png" /></figure>

* EMBL EST of Triticeae

<figure><img src="image_51.png" /></figure>

* FgeneSH predictions
o Impact of annotation methods on knowledge

➤ in 2017: 3 versions of Chinese Spring chr3B

chr3B BAC-by-BAC

<figure><img src="image_52.png" /></figure>

Choulet et al. Science 2014

TGAC_v1

<figure><img src="image_53.png" /></figure>

Clavijo et al. Genom Biol 2017

Chr. Survey Seq

<figure><img src="image_54.png" /></figure>

IWGSC Science 2014

7264 genes

5728 genes
-> (26% identical)

5862 genes
(12% identical)
## A-B-D Comparative Genomics

HC

35345

35643

34212

107k

<figure><img src="image_55.png" /></figure>

<figure><img src="image_56.png" /></figure>

<figure><img src="image_57.png" /></figure>

35k HC genes

36k

34k

<figure><img src="image_58.png" /></figure>

<figure><img src="image_59.png" /></figure>

### 39k homeologous groups [ including 29k LC genes ]

A B D

<figure><img src="image_60.png" /></figure>

55% 1:1:1 triads

<figure><img src="image_61.png" /></figure>

15% N:1:1 (duplications)

<figure><img src="image_62.png" /></figure>

30% 0:1:1 11%
1:0:1 10%
1:1:0 9%

[ 27% of genes are duplicates ]
ex: 207 PPRs
o Polyploidy + single gene duplications

<figure><img src="image_63.png" /></figure>

<figure><img src="image_64.png" /></figure>
3. A-B-D Comparative Analysis of TEs

Wicker et al. Genome Biology (2018) 19:103
https://doi.org/10.1186/s13059-018-1479-0

Genome Biology

RESEARCH

Open Access

<figure><img src="image_65.png" /></figure>

CrossMark

Impact of transposable elements on
genome structure and evolution in bread
wheat

Thomas Wicker¹†, Heidrun Gundlach²†, Manuel Spannagl², Cristobal Uauy³, Philippa Borrill³, Ricardo H. Ramírez-González³, Romain De Oliveira⁴, International Wheat Genome Sequencing Consortium⁵, Klaus F. X. Mayer²,⁶, Etienne Paux⁴ and Frédéric Choulet⁴*
○ TE modeling with CLARI-TE and ClariTeRep

https://github.com/jdaron/CLARI-TE

<figure><img src="image_66.png" /></figure>

<figure><img src="image_67.png" /></figure>

~5000 known wheat TEs

<figure><img src="image_68.png" /></figure>

Classification

<figure><img src="image_69.png" /></figure>

<figure><img src="image_70.png" /></figure>

ClariTeRep

<figure><img src="image_71.png" /></figure>

~500 families
<figure><img src="image_72.png" /><figcaption>TE insertions</figcaption></figure>

<figure><img src="image_73.png" /></figure>
<figure><img src="image_74.png" /><figcaption>> Near-complete **TE turnover** since A-B-D divergence</figcaption></figure>
o % TEs

<figure><img src="image_75.png" /><figcaption>Families</figcaption></figure>

➤ Abundant families are the same on A-B-D

➤ 0 family specific to 1 subgenome

➤ 76% of the fam. account for similar %
on A-B-D (<2 fold-change)
o TE trees

<figure><img src="image_76.png" /></figure>

Family#3

<figure><img src="image_77.png" /></figure>

➤ Independent TE evolution in the diploids AA, BB, DD

➤ Some rare cases of TE amplif in the tetraploid ABB
o TE content around genes

<figure><img src="image_78.png" /></figure>

<figure><img src="image_79.png" /></figure>

> Wide majority of TE families either enriched/underrepres. in gene promoters

> Enrichment/Underrepres. close to genes is conserved betw A-B-D

<figure><img src="image_80.png" /></figure>
## ○ TE dynamics

- Most families were active

- **Equilibrium**

-> Hypothesis of a **structural role of TEs likely under selection pressure?**

<figure><img src="image_81.png" /></figure>

<figure><img src="image_82.png" /></figure>

<figure><img src="image_83.png" /></figure>

<figure><img src="image_84.png" /></figure>
# 4. Structural Variations in *Triticum* using resequencing data

PhD Romain De Oliveira

<figure><img src="image_85.png" /></figure>

<figure><img src="image_86.png" /></figure>

## Structural Variations Affecting Genes and Transposable Elements of Chromosome 3B in Wheats

Romain De Oliveira¹, Hélène Rimbert¹, François Balfourier¹, Jonathan Kitt¹, Emeric Dynomant¹, Jan Vrána², Jaroslav Doležel², Federica Cattonaro³, Etienne Paux¹ and Frédéric Choulet¹*
45 accessions / 7 species

-> sorted 3B DNA

<figure><img src="image_87.png" /></figure>

<figure><img src="image_88.png" /></figure>

3B

<figure><img src="image_89.png" /></figure>

850 Mb

<figure><img src="image_90.png" /></figure>

<figure><img src="image_91.png" /></figure>

Illumina reseq ~30x

<figure><img src="image_92.png" /></figure>

T. aestivum (Asia)

T. aestivum (others)

T. spelta

T. carthlicum

T. macha

T. durum

T. dicoccum

T. dicoccoides
AccessionX

<figure><img src="image_93.png" /></figure>

Chinese Spring

<figure><img src="image_94.png" /></figure>

$$ \log_2 \frac{\text{COV}^{\text{accX}}}{\text{COV}^{\text{ChineseSpring}}} $$

CNVs

<figure><img src="image_95.png" /></figure>
<figure><img src="image_96.png" /></figure>

<figure><img src="image_97.png" /></figure>

Chromosome 3B

~7000 genes

PAVs/CNVs: **20%** core=**80%**
new genes: **330**

<figure><img src="image_98.png" /></figure>

* functions: related to stress response

* expressed in more specific conditions
○ TE CNVs

<figure><img src="image_99.png" /></figure>

<figure><img src="image_100.png" /></figure>

Chinese Spring chr3B
~500 TE families
○ **TE CNVs**

TE% = **84%** in all 45 accessions

<figure><img src="image_101.png" /></figure>

➤ No major difference of the number of TE copies for each superfamily
○ **TE CNVs**

<figure><img src="image_102.png" /></figure>

0 fam with log2ratio > 2

➤ At the family level: globally extremely conserved proportions
## ○ TE PAVs

<figure><img src="image_103.png" /></figure>

<figure><img src="image_104.png" /></figure>

1 ISBP every 3 kb

<figure><img src="image_105.png" /></figure>

RESULTS for 45 *Triticum* accessions:

- from **7%** to **19%** TE-PAVs

- cumulated variable: **60% ISBPs**
○ TE PAVs – distribution of polymorphisms

<figure><img src="image_106.png" /></figure>
# 5. Genomic variability affecting **TEs** in wheat **using assembled genomes**

PhD Nathan Papon (2019-2022)

* Methodology for comparative genomics of complex genomes with Gbps of repeats

* Extent of genomic variability?

* Active families? Amount of transposition events?

* Did polyploidization trigger a TE burst?
Triticum
aestivum

<figure><img src="image_107.png" /></figure>

<figure><img src="image_108.png" /></figure>

Triticum
dicoccoides

<figure><img src="image_109.png" /></figure>

<figure><img src="image_110.png" /></figure>

Triticum
urartu

<figure><img src="image_111.png" /></figure>

<figure><img src="image_112.png" /></figure>

Aegilops
tauschii

<figure><img src="image_113.png" /></figure>

<figure><img src="image_114.png" /></figure>

<figure><img src="image_115.png" /></figure>

Multiple RefSeq now available
<figure><img src="image_116.png" /></figure>

<figure><img src="image_117.png" /></figure>

<figure><img src="image_118.png" /></figure>
<figure><img src="image_119.png" /></figure>

Results:

Variable regions represent (pairwise):

- inter-specific: 8-34% of the sequences

- intra-specific: 4-6% of the sequences
<figure><img src="image_120.png" /></figure>

Extent of variability due to recent insertions?

➤ ~5k-10k transposition events / subgenome (<1% of the genome)

➤ 238 active families

Impact of polyploidy?

➤ none

<figure><img src="image_121.png" /></figure>

➤ Equilibrium
6. Sequencing the Renan genome

<figure><img src="image_122.png" /></figure>

GigaScience, 2022, 11, 1–18

DOI: 10.1093/gigascience/giac034

RESEARCH

Long-read and chromosome-scale assembly of the
hexaploid wheat genome achieves high resolution for
research and breeding

Jean-Marc Aury Ⓓ1,*, Stefan Engelen Ⓓ1, Benjamin Istace Ⓓ1, Cécile Monat Ⓓ2, Pauline Lasserre-Zuber², Caroline Belser Ⓓ1,
Corinne Cruaud Ⓓ3, Hélène Rimbert Ⓓ2, Philippe Leroy Ⓓ2, Sandrine Arribat Ⓓ4, Isabelle Dufau⁴, Arnaud Bellec Ⓓ4,
David Grimbichler Ⓓ5, Nathan Papon², Etienne Paux Ⓓ2, Marion Ranoux², Adriana Alberti Ⓓ1,⁶, Patrick Wincker Ⓓ1 and
Frédéric Choulet Ⓓ2,.*
Yr17 Lr37
Sr38 Cre5

<figure><img src="image_123.png" /></figure>

T. aestivum
Renan

Pch1

<figure><img src="image_124.png" /></figure>

<figure><img src="image_125.png" /></figure>

Ae. ventricosa
o Genome Assembly

<figure><img src="image_126.png" /></figure>

o Annotation of genes

<figure><img src="image_127.png" /></figure>

~12% ambiguous mapping

* *denovo* gene annotation would generate to many differences

* gene mapping from a reference is NOT satisfying

➤ Develop **MAGATT**
<figure><img src="image_128.png" /></figure>

# MAGATT (Marker-Assisted Gene Annotation Transfer for *Triticeae*)

<figure><img src="image_129.png" /></figure>

* 98% of genes mapped accurately

* +4400 Renan specific genes
□ Introgressions

<figure><img src="image_130.png" /></figure>

telomere

Renan

40 Mb

chr2N

chr2A

<figure><img src="image_131.png" /></figure>

telomere

Chinese Spring

35 Mb

<figure><img src="image_132.png" /></figure>
<figure><img src="image_133.png" /><figcaption>Renan - chr7D<sup>V</sup></figcaption></figure>

telomere

<figure><img src="image_134.png" /><figcaption>Chinese Spring - chr7D</figcaption></figure>

30 Mb, ~500 genes

<figure><img src="image_135.png" /><figcaption>Renan - chr7D<sup>V</sup></figcaption></figure>

<caption>Chinese Spring - chr7D</caption>

➤ Introgressions: source of diversity in modern breeding lines

analyses in progress...
## Conclusions

* Wheat has reached the pangenomic area

* Annotation matters

## Perspectives

* Build a wheat pangenome based on 8-12 founder lines

* IWGSC/NSF proposal under review

* GDEC, IPS2

<figure><img src="image_136.png" /></figure>

<figure><img src="image_137.png" /></figure>

STRUCTURE

<figure><img src="image_138.png" /></figure>
□ Acknowledgments

o GDEC, INRAE, UCA, Clermont-Fd

Nathan Papon
Romain De Oliveira
Cécile Monat
Caroline Juery
Josquin Daron
Emeric Dynomant
Hélène Rimbert
Philippe Leroy
Pauline Lasserre-Zuber
Jonathan Kitt
Marion Ranoux
Florence Exbrayat
François Balfourier
Etienne Paux
Pierre Sourdille
Sophie Bouchet

o Collaborators

Jean-Marc Aury's team (Genoscope)
Arnaud Bellec (INRAE CNRGV)
Michael Alaux (INRAE URGI)
Thomas Wicker (U Zurich)
Heidrun Gundlach (PGSB Munich)
Manuel Spannagl (PGSB Munich)
Jan Vrana (IEB Olomouc)
Jaroslav Dolezel (IEB Olomouc)
Federica Cattonaro (IGA, Udine)

o IWGSC

K. Eversole, et al.