Journal Article

A pan-genome of 69 Arabidopsis thaliana accessions reveals a conserved genome structure throughout the global species range

Roux, Fabrice, Ludwig Maximilian University [Munich] = Ludwig Maximilians Universität München (LMU), Mayjonade, Baptiste, Lian, Qichao, This work was supported by core funding from the Max Planck Society and an Alexander von Humboldt Fellowship to Q.L. This work was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany's Excellence Strategy-EXC 2048/1-390686111 (to K.S. and R.M.) and TRR 341/1-456082119 to K.S., as well as by the European Research Council (ERC) with the grant 'INTERACT' to K.S, Max Planck Institute for Plant Breeding Research (MPIPZ), Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe) ; Plateforme Génome & Transcriptome (GET) ; Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL) ; Université Toulouse III - Paul Sabatier (UT3) ; Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT) ; Institut National Polytechnique (Toulouse) (Toulouse INP) ; Université de Toulouse (UT)-Université de

2024

Overview

Although originally primarily a system for functional biology, Arabidopsis thaliana has, owing to its broad geographical distribution and adaptation to diverse environments, developed into a powerful model in population genomics. Here we present chromosome-level genome assemblies of 69 accessions from a global species range. We found that genomic colinearity is very conserved, even among geographically and genetically distant accessions. Along chromosome arms, megabase-scale rearrangements are rare and typically present only in a single accession. This indicates that the karyotype is quasi-fixed and that rearrangements in chromosome arms are counter-selected. Centromeric regions display higher structural dynamics, and divergences in core centromeres account for most of the genome size variations. Pan-genome analyses uncovered 32,986 distinct gene families, 60% being present in all accessions and 40% appearing to be dispensable, including 18% private to a single accession, indicating unexplored genic diversity. These 69 new Arabidopsis thaliana genome assemblies will empower future genetic research.

• Publisher: Nature Publishing Group,CCSD,Nature Publishing Group US
• Subject: 631/208/191 / 631/208/212 / 631/449/1659 / Agriculture / Animal Genetics and Genomics / Arabidopsis / Arabidopsis - genetics / Artificial chromosomes / Assemblies / Biochemistry, Molecular Biology / Biomedical and Life Sciences / Biomedicine / Cancer Research / Centromere - genetics / Centromeres / Chromosomes / Chromosomes, Plant - genetics / Evolution, Molecular / Flow cytometry / Gene families / Gene Function / Genetic diversity / Genetic Variation / Genetics / Genome, Plant / Genomes / Genomics / Genomics - methods / Geographical distribution / Human Genetics / Karyotypes / Life Sciences / Phylogeny / Plants genetics / Ribosomal DNA
• ISBN: 0012007379000