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.

Agroécologie AgroSup Dijon INRA Université Bourgogne Franche Comté Bourgogne Université Bourgogne Franche Comté Dijon France

Biology Centre Czech Academy of Sciences České Budějovice Czech Republic

Centre for Crop and Disease Management Curtin University Bentley Western Australia Australia

Centre for Crop and Disease Management School of Molecular and Life Science Curtin University Bentley Western Australia Australia

Crop Development Centre Department of Plant Sciences University of Saskatchewan Saskatoon Saskatchewan Canada

Department of Horticulture Washington State University Pullman WA USA

Department of Plant Breeding IFZ Research Centre for Biosystems Land Use and Nutrition Justus Liebig University Giessen Germany

Etude du Polymorphisme des Génomes Végétaux INRA Université Paris Saclay Evry France

Génomique Métabolique Genoscope Institut François Jacob CEA CNRS Université Evry Université Paris Saclay Evry France

Genoscope Institut François Jacob CEA Université Paris Saclay Evry France

GQE Le Moulon INRA University of Paris Sud CNRS AgroParisTech Université Paris Saclay Gif sur Yvette France

Institute of Experimental Botany Centre of the Region Haná for Biotechnological and Agricultural Research Olomouc Czech Republic

Institute of Plant Sciences Paris Saclay INRA CNRS University of Paris Sud University of Evry University Paris Diderot Sorbonne Paris Cite University of Paris Saclay Orsay France

School of Agriculture and Environment University of Western Australia Perth Western Australia Australia

School of Biological Sciences and Institute of Agriculture University of Western Australia Perth Western Australia Australia

School of Biological Sciences University of Auckland Auckland New Zealand

UMR 1095 Génétique Diversité Ecophysiologie des Céréales INRA Université Clermont Auvergne Clermont Ferrand France

URGI INRA Université Paris Saclay Versailles France

USDA Agricultural Research Service Pullman WA USA

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