A reference genome for pea provides insight into legume genome evolution

Authors: KREPLAK, JONATHAN - Inland Northwest Research Alliance, Inra; MADOUI, MD-AMIN - National Council For Scientific Research-Cnrs; CAPAL, PETR - Institute Of Experimental Botany; NOVAK, PETR - Biology Centre Of The Ascr Of The Czech Republic, Vvi; LABADIE, KARINE - Université Paris-Saclay; AUBERT, GREGOIRE - Inland Northwest Research Alliance, Inra; BAYER, PHILLIP - Wagga Wagga Agricultural Institute; KRISHNA-KISHORE, GALI - University Of Saskatchewan; SYMES, ROBERT - Curtin University; MAIN, DORRIE - Washington State University; KLEIN, ANTHONY - Inra, Génétique Animale Et Biologie Intégrative , Jouy-En-josas, France; BERARD, AURELIE - Inra, Génétique Animale Et Biologie Intégrative , Jouy-En-josas, France; FUKOVA, IVA - Biology Centre Of The Ascr Of The Czech Republic, Vvi; FOURNIER, CRYIL - Inra, Génétique Animale Et Biologie Intégrative , Jouy-En-josas, France; D'AGATA, LEO - Genoscope; BELSER, CAROLINE - Genoscope; BERRABAH, WAHIBA - Genoscope; SIMKOVA, HANA - Institute Of Experimental Botany; LEE, HUEY - University Of Western Australia; KOUGBEAD, AYITE - Inra, Génétique Animale Et Biologie Intégrative , Jouy-En-josas, France; TEREZOL, MORGANE - Inra, Génétique Animale Et Biologie Intégrative , Jouy-En-josas, France; HUNEAU, CECILE - Inra, Génétique Animale Et Biologie Intégrative , Jouy-En-josas, France; TURO, CHALA - Curtin University; MOHELLIBI, NACER - Inra, Génétique Animale Et Biologie Intégrative , Jouy-En-josas, France; NEUMANN, PAVEL - Institute Of Experimental Biology; FALQUE, MATTHIEU - Inra, Génétique Animale Et Biologie Intégrative , Jouy-En-josas, France; GALLARDO-GUERRERO, KARINE - Inra, Génétique Animale Et Biologie Intégrative , Jouy-En-josas, France; McGee, Rebecca; TAR'AN, BUNYAMIN - University Of Saskatchewan; BENDAHMANE, ABDELHAFID - Inra, Génétique Animale Et Biologie Intégrative , Jouy-En-josas, France; AURY, JEAN-MARC - Genoscope; BATLEY, JACQUI - Wagga Wagga Agricultural Institute; LE PASLIER, MARIE-CHRISTINE - Inra, Génétique Animale Et Biologie Intégrative , Jouy-En-josas, France; ELLIS, TH NOEL - University Of Auckland; WARKENTIN, TOM - University Of Saskatchewan; Coyne, Clarice - Clare; SALSE, JEROME - Inra, Génétique Animale Et Biologie Intégrative , Jouy-En-josas, France; EDWARDS, DAVE - Wagga Wagga Agricultural Institute; LICHTENZVEIG, JUDITH - University Of Western Australia; MACAS, JIRI - Biology Centre Of The Ascr Of The Czech Republic, Vvi; DOLEZEL, JAROSLAV - Institute Of Experimental Botany; WINCKER, PATRICK - Genoscope; BURSTIN, JUDITH - Inra, Génétique Animale Et Biologie Intégrative , Jouy-En-josas, France

Submitted to: Nature Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/10/2019
Publication Date: 9/2/2019
Citation: Kreplak, J., Madoui, M., Capal, P., Novak, P., Labadie, K., Aubert, G., Bayer, P., Krishna-Kishore, G., Symes, R.A., Main, D., Klein, A., Berard, A., Fukova, I., Fournier, C., D'Agata, L., Belser, C., Berrabah, W., Simkova, H., Lee, H.T., Kougbead, A., Terezol, M., Huneau, C., Turo, C.J., Mohellibi, N., Neumann, P., Falque, M., Gallardo-Guerrero, K., McGee, R.J., Tar'An, B., Bendahmane, A., Aury, J., Batley, J., Le Paslier, M., Ellis, T., Warkentin, T., Coyne, C.J., Salse, J., Edwards, D., Lichtenzveig, J., Macas, J., Dolezel, J., Wincker, P., Burstin, J. 2019. A reference genome for pea provides insight into legume genome evolution. Nature Genetics. 51:1411-1422. https://doi.org/10.1038/s41588-019-0480-1.
DOI: https://doi.org/10.1038/s41588-019-0480-1

Interpretive Summary: A major objective in pulse crop research is to develop an accurate genome sequence. This can be used by all research scientists as a 'road map' to identify genes that control characteristics of interest and to understand their mode of action. This study, by an international consortium of researchers, reports the first annotated reference genome sequence for pea. Pea has long been a model for genetic studies, in 1865 Gregor Mendel, an Augustinian monk, reported on experiments concerning the heredity of characteristics in peas that led him to formulate the laws of inheritance that are the foundation of modern genetics. This genome sequence will be valuable for plant breeders in the development of new pea cultivars with improved traits such as disease tolerance and resistance to heat and drought stress. The sequence will also be valuable to plant physiologists, evolutionary biologists and other researchers who work with pea. Researchers will be able to freely access the genome sequences on the Cool Season Food Legume Database (www.coolseasonfoodlegume.org).

Technical Abstract: Here we report the first annotated chromosome-level reference genome assembly for pea, the legume species established by Gregor Mendel as the first model plant in genetics. Phylogenetics and paleogenomics demonstrate re-arrangements across legume genomes and suggest a major role of repetitive elements in pea genome evolution. Compared with other sequenced Leguminosae genomes, the pea genome shows active gene gain and gene loss most likely associated with genome size expansion about the time of the Fabeae’s divergence from sister tribes. During Pisum evolution, translocation and transposition activity differentially occurred in the divergent lineages. This reference sequence will accelerate our understanding of the molecular basis of agronomically important traits and support their translation into crop improvement. The genome sequence and annotations are publically available on the Cool Season Food Legume Database (www.coolseasonfoodlegume.org).