Genome Bioinformatics at GDEC

Frédéric Choulet

► To cite this version:

Frédéric Choulet. Genome Bioinformatics at GDEC. AuBi-NGS Annual Meeting, AuBi - Auvergne Bioinformatique, Dec 2022, Clermont-Ferrand, France. hal-04090099

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Submitted on 5 May 2023

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Distributed under a Creative Commons Attribution - ShareAlike 4.0 International License
# Genome Bioinformatics at GDEC

Frédéric Choulet

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UNIVERSITÉ
Clermont
Auvergne
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<figure><img src="image_5.png" /><figcaption>○ Bioinfo for bread wheat and *Triticeae* (pan)genomics</figcaption></figure>

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❖ Research area and questions

o Methodologies

- Gene and transposon prediction in genomes

- Comparative genomics

- How to compare “complex” genomes?

o Genome Biology

- What is the extent of diversity? Pangenomics

- What is the dynamics of transposons?

- What is the impact of polyploidy on transposon activity?

- ...
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15 Gb

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Triticum/Aegilops

- Wild **diploids** (AA, BB, DD, SS, UU, NN, ...)

- Wild & cultivated **tetraploids** (AABB, DDNN, ...)

- Cultivated **hexaploids** (AABBDD)

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❖ Genome composition

○ Transposons (85%)

o Genes (2%)

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1st genome seq assembled:
**Chinese Spring** (IWGSC Science 2018)

○ 4 million TEs

○ ~107,000 genes
Pangenomics

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* T. aestivum

* Chinese Spring (Illumina)

* 10 other varieties (Illumina)

* Zang1817 (Illumina)

* Fielder (Pacbio)

* Kariega (Pacbio)

* Renan (ONT)

* Attraktion (Pacbio)

IWGSC 2018

Walkowiak et al. 2020

Guo et al. 2020

Sato et al. 2021

Athiyannan et al. 2022

Aury et al. 2022

Kale et al. 2022

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* T. durumABB

* T. dicoccoides ABB

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* T. urartu AA

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* Ae. tauschii DD

* Ae. searsii DD

* Ae. bicornis DD

* Ae. longissima DD

* Ae. sharonensis DD

* Ae. speltoides SS

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=pangenome
Pangenomics

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Chromosome-scale assemblies required

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

Jean-Marc Auray,¹,*, Stefan Engelen,¹, Benjamin Istace,¹, Cécile Monat,², Pauline Lasserre-Zuber,¹, Caroline Belser,¹,

Corinne Cruaud,¹, Hélène Rimbert,², Philippe Leroy,², Sandrine Arribat,¹, Isabelle Dufaux,¹, Arnaud Bellet,¹,

David Grimbichler,¹, Nathan Papon,¹, Etienne Paux,², Marion Ranoux,², Adriana Alberti,¹,², Patrick Wincker,¹ and

Frédéric Choulet,¹,•

<figure><img src="image_22.png" /><figcaption>Chinese Spring</figcaption></figure>

<figure><img src="image_23.png" /><figcaption>Renan</figcaption></figure>

✓ Nanopore

✓ Illumina

✓ Bionano

✓ HiC

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## Genes
o Predicting genes is not trivial

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de novo gene prediction not adapted to pangenomics

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❖ Gene annotation

o Predicting genes is not trivial

➤ de novo gene prediction not adapted to pangenomics

o Mapping a reference gene set sounds better

➤ Develop **MAGATT** (H. Rimbert)

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Chinese Spring

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Renan

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107k genes

Gmap

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88% of genes
mapped
unambiguously
❖ Gene annotation

o Predicting genes is not trivial

➤ de novo gene prediction not adapted to pangenomics

o Mapping a reference gene set sounds better

➤ Develop **MAGATT** (*H. Rimbert*)

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❖ Gene annotation

o Predicting genes is not trivial

➤ de novo gene prediction not adapted to pangenomics

o Mapping a reference gene set sounds better

➤ Develop **MAGATT** (H. Rimbert)

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Chinese Spring

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Renan

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107k genes

Gmap

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88% of genes
mapped
unambiguously

MAGATT

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98% of genes
mapped
unambiguously
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Transposons
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➢ Equilibrium model of evolution

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PhD Nathan Papon (2019-2023)

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Method: bp-resolved gene anchored whole-genome transposition

* How variable is the TE space?

➤ 5 .. 15%

* Which TE families are active?

➤ ~ all

* Impact of polyploidization?

➤ none

➤ Transposition highly regulated; transposons may be essential for shaping a functional genome architecture

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## ❖ Acknowledgments

### ○ GDEC, INRAE, UCA, Clermont-Fd

- Nathan Papon

- Hélène Rimbert

- Pauline Lasserre-Zuber

- Philippe Leroy

- Romain De Oliveira

- Cécile Monat

- Jonathan Kitt

- Marion Ranoux

- Florence Exbrayat

- François Balfourier

- Etienne Paux

- Pierre Sourdille

- Sophie Bouchet

### ○ 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)

### ○ IWGSC

- Kellye Eversole, et al.

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Contact:
frederic.choulet@inrae.fr

### ○ Funding

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FRANCE
GENOMIQUE

SRESRI/Région ARA

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L'EUROPE S'ENGAGE
en région
Auvergne-Rhône-Alpes
muni de FEDER

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La Région
Auvergne-Rhône-Alpes

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UNIVERSITÉ
Clermont
Auvergne

INRAE