A reference genome for pea provides insight into legume genome evolution

Jonathan Kreplak, Mohammed Amin Madoui, Petr Cápal, Petr Novák, Karine Labadie, Grégoire Aubert, Philipp E. Bayer, Krishna K. Gali, Robert A. Syme, Dorrie Main, Anthony Klein, Aurélie Bérard, Iva Vrbová, Cyril Fournier, Leo d’Agata, Caroline Belser, Wahiba Berrabah, Helena Toegelová, Zbyněk Milec, Jan Vrána & 25 others Huey Tyng Lee, Ayité Kougbeadjo, Morgane Térézol, Cécile Huneau, Chala J. Turo, Nacer Mohellibi, Pavel Neumann, Matthieu Falque, Karine Gallardo, Rebecca McGee, Bunyamin Tar’an, Abdelhafid Bendahmane, Jean Marc Aury, Jacqueline Batley, Marie Christine Le Paslier, Noel Ellis, Thomas D. Warkentin, Clarice J. Coyne, Jérome Salse, David Edwards, Judith Lichtenzveig, Jiří Macas, Jaroslav Doležel, Patrick Wincker, Judith Burstin

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

We report the first annotated chromosome-level reference genome assembly for pea, Gregor Mendel’s original genetic model. Phylogenetics and paleogenomics show genomic rearrangements across legumes and suggest a major role for repetitive elements in pea genome evolution. Compared to other sequenced Leguminosae genomes, the pea genome shows intense gene dynamics, most likely associated with genome size expansion when the Fabeae diverged from its sister tribes. During Pisum evolution, translocation and transposition differentially occurred across lineages. This reference sequence will accelerate our understanding of the molecular basis of agronomically important traits and support crop improvement.

Original languageEnglish
Pages (from-to)1411-1422
Number of pages12
JournalNature Genetics
Volume51
Issue number9
DOIs
Publication statusPublished - 2 Sep 2019

Fingerprint

Peas
Fabaceae
Genome
Genome Size
Genetic Models
Chromosomes
Genes

Cite this

Kreplak, J., Madoui, M. A., Cápal, P., Novák, P., Labadie, K., Aubert, G., ... Burstin, J. (2019). A reference genome for pea provides insight into legume genome evolution. Nature Genetics, 51(9), 1411-1422. https://doi.org/10.1038/s41588-019-0480-1
Kreplak, Jonathan ; Madoui, Mohammed Amin ; Cápal, Petr ; Novák, Petr ; Labadie, Karine ; Aubert, Grégoire ; Bayer, Philipp E. ; Gali, Krishna K. ; Syme, Robert A. ; Main, Dorrie ; Klein, Anthony ; Bérard, Aurélie ; Vrbová, Iva ; Fournier, Cyril ; d’Agata, Leo ; Belser, Caroline ; Berrabah, Wahiba ; Toegelová, Helena ; Milec, Zbyněk ; Vrána, Jan ; Lee, Huey Tyng ; Kougbeadjo, Ayité ; Térézol, Morgane ; Huneau, Cécile ; Turo, Chala J. ; Mohellibi, Nacer ; Neumann, Pavel ; Falque, Matthieu ; Gallardo, Karine ; McGee, Rebecca ; Tar’an, Bunyamin ; Bendahmane, Abdelhafid ; Aury, Jean Marc ; Batley, Jacqueline ; Le Paslier, Marie Christine ; Ellis, Noel ; Warkentin, Thomas D. ; Coyne, Clarice J. ; Salse, Jérome ; Edwards, David ; Lichtenzveig, Judith ; Macas, Jiří ; Doležel, Jaroslav ; Wincker, Patrick ; Burstin, Judith. / A reference genome for pea provides insight into legume genome evolution. In: Nature Genetics. 2019 ; Vol. 51, No. 9. pp. 1411-1422.
@article{957556924a8a4db8bccb6904fd3c118d,
title = "A reference genome for pea provides insight into legume genome evolution",
abstract = "We report the first annotated chromosome-level reference genome assembly for pea, Gregor Mendel’s original genetic model. Phylogenetics and paleogenomics show genomic rearrangements across legumes and suggest a major role for repetitive elements in pea genome evolution. Compared to other sequenced Leguminosae genomes, the pea genome shows intense gene dynamics, most likely associated with genome size expansion when the Fabeae diverged from its sister tribes. During Pisum evolution, translocation and transposition differentially occurred across lineages. This reference sequence will accelerate our understanding of the molecular basis of agronomically important traits and support crop improvement.",
author = "Jonathan Kreplak and Madoui, {Mohammed Amin} and Petr C{\'a}pal and Petr Nov{\'a}k and Karine Labadie and Gr{\'e}goire Aubert and Bayer, {Philipp E.} and Gali, {Krishna K.} and Syme, {Robert A.} and Dorrie Main and Anthony Klein and Aur{\'e}lie B{\'e}rard and Iva Vrbov{\'a} and Cyril Fournier and Leo d’Agata and Caroline Belser and Wahiba Berrabah and Helena Toegelov{\'a} and Zbyněk Milec and Jan Vr{\'a}na and Lee, {Huey Tyng} and Ayit{\'e} Kougbeadjo and Morgane T{\'e}r{\'e}zol and C{\'e}cile Huneau and Turo, {Chala J.} and Nacer Mohellibi and Pavel Neumann and Matthieu Falque and Karine Gallardo and Rebecca McGee and Bunyamin Tar’an and Abdelhafid Bendahmane and Aury, {Jean Marc} and Jacqueline Batley and {Le Paslier}, {Marie Christine} and Noel Ellis and Warkentin, {Thomas D.} and Coyne, {Clarice J.} and J{\'e}rome Salse and David Edwards and Judith Lichtenzveig and Jiř{\'i} Macas and Jaroslav Doležel and Patrick Wincker and Judith Burstin",
year = "2019",
month = "9",
day = "2",
doi = "10.1038/s41588-019-0480-1",
language = "English",
volume = "51",
pages = "1411--1422",
journal = "Nature Genetics",
issn = "1061-4036",
publisher = "Nature Publishing Group - Macmillan Publishers",
number = "9",

}

Kreplak, J, Madoui, MA, Cápal, P, Novák, P, Labadie, K, Aubert, G, Bayer, PE, Gali, KK, Syme, RA, Main, D, Klein, A, Bérard, A, Vrbová, I, Fournier, C, d’Agata, L, Belser, C, Berrabah, W, Toegelová, H, Milec, Z, Vrána, J, Lee, HT, Kougbeadjo, A, Térézol, M, Huneau, C, Turo, CJ, Mohellibi, N, Neumann, P, Falque, M, Gallardo, K, McGee, R, Tar’an, B, Bendahmane, A, Aury, JM, Batley, J, Le Paslier, MC, Ellis, N, Warkentin, TD, Coyne, CJ, Salse, J, Edwards, D, Lichtenzveig, J, Macas, J, Doležel, J, Wincker, P & Burstin, J 2019, 'A reference genome for pea provides insight into legume genome evolution' Nature Genetics, vol. 51, no. 9, pp. 1411-1422. https://doi.org/10.1038/s41588-019-0480-1

A reference genome for pea provides insight into legume genome evolution. / Kreplak, Jonathan; Madoui, Mohammed Amin; Cápal, Petr; Novák, Petr; Labadie, Karine; Aubert, Grégoire; Bayer, Philipp E.; Gali, Krishna K.; Syme, Robert A.; Main, Dorrie; Klein, Anthony; Bérard, Aurélie; Vrbová, Iva; Fournier, Cyril; d’Agata, Leo; Belser, Caroline; Berrabah, Wahiba; Toegelová, Helena; Milec, Zbyněk; Vrána, Jan; Lee, Huey Tyng; Kougbeadjo, Ayité; Térézol, Morgane; Huneau, Cécile; Turo, Chala J.; Mohellibi, Nacer; Neumann, Pavel; Falque, Matthieu; Gallardo, Karine; McGee, Rebecca; Tar’an, Bunyamin; Bendahmane, Abdelhafid; Aury, Jean Marc; Batley, Jacqueline; Le Paslier, Marie Christine; Ellis, Noel; Warkentin, Thomas D.; Coyne, Clarice J.; Salse, Jérome; Edwards, David; Lichtenzveig, Judith; Macas, Jiří; Doležel, Jaroslav; Wincker, Patrick; Burstin, Judith.

In: Nature Genetics, Vol. 51, No. 9, 02.09.2019, p. 1411-1422.

Research output: Contribution to journalArticle

TY - JOUR

T1 - A reference genome for pea provides insight into legume genome evolution

AU - Kreplak, Jonathan

AU - Madoui, Mohammed Amin

AU - Cápal, Petr

AU - Novák, Petr

AU - Labadie, Karine

AU - Aubert, Grégoire

AU - Bayer, Philipp E.

AU - Gali, Krishna K.

AU - Syme, Robert A.

AU - Main, Dorrie

AU - Klein, Anthony

AU - Bérard, Aurélie

AU - Vrbová, Iva

AU - Fournier, Cyril

AU - d’Agata, Leo

AU - Belser, Caroline

AU - Berrabah, Wahiba

AU - Toegelová, Helena

AU - Milec, Zbyněk

AU - Vrána, Jan

AU - Lee, Huey Tyng

AU - Kougbeadjo, Ayité

AU - Térézol, Morgane

AU - Huneau, Cécile

AU - Turo, Chala J.

AU - Mohellibi, Nacer

AU - Neumann, Pavel

AU - Falque, Matthieu

AU - Gallardo, Karine

AU - McGee, Rebecca

AU - Tar’an, Bunyamin

AU - Bendahmane, Abdelhafid

AU - Aury, Jean Marc

AU - Batley, Jacqueline

AU - Le Paslier, Marie Christine

AU - Ellis, Noel

AU - Warkentin, Thomas D.

AU - Coyne, Clarice J.

AU - Salse, Jérome

AU - Edwards, David

AU - Lichtenzveig, Judith

AU - Macas, Jiří

AU - Doležel, Jaroslav

AU - Wincker, Patrick

AU - Burstin, Judith

PY - 2019/9/2

Y1 - 2019/9/2

N2 - We report the first annotated chromosome-level reference genome assembly for pea, Gregor Mendel’s original genetic model. Phylogenetics and paleogenomics show genomic rearrangements across legumes and suggest a major role for repetitive elements in pea genome evolution. Compared to other sequenced Leguminosae genomes, the pea genome shows intense gene dynamics, most likely associated with genome size expansion when the Fabeae diverged from its sister tribes. During Pisum evolution, translocation and transposition differentially occurred across lineages. This reference sequence will accelerate our understanding of the molecular basis of agronomically important traits and support crop improvement.

AB - We report the first annotated chromosome-level reference genome assembly for pea, Gregor Mendel’s original genetic model. Phylogenetics and paleogenomics show genomic rearrangements across legumes and suggest a major role for repetitive elements in pea genome evolution. Compared to other sequenced Leguminosae genomes, the pea genome shows intense gene dynamics, most likely associated with genome size expansion when the Fabeae diverged from its sister tribes. During Pisum evolution, translocation and transposition differentially occurred across lineages. This reference sequence will accelerate our understanding of the molecular basis of agronomically important traits and support crop improvement.

UR - http://www.scopus.com/inward/record.url?scp=85071767701&partnerID=8YFLogxK

U2 - 10.1038/s41588-019-0480-1

DO - 10.1038/s41588-019-0480-1

M3 - Article

VL - 51

SP - 1411

EP - 1422

JO - Nature Genetics

JF - Nature Genetics

SN - 1061-4036

IS - 9

ER -

Kreplak J, Madoui MA, Cápal P, Novák P, Labadie K, Aubert G et al. A reference genome for pea provides insight into legume genome evolution. Nature Genetics. 2019 Sep 2;51(9):1411-1422. https://doi.org/10.1038/s41588-019-0480-1