Oryza genome evolution through a tetraploid lens
Oryza is a remarkable genus comprising 27 species and 11 genome types, with ~3.4-fold genome size variation, that possesses a virtually untapped reservoir of genes that can be used for crop improvement and neodomestication. Here we present 11 chromosome-level assemblies (nine tetraploid, two diploid) in the context of ~15 million years of evolution and show that the core Oryza (sub)genome is only ~200 Mb and largely syntenic, whereas the remaining nuclear fractions (~80-600 Mb) are intermingled, plastic and rapidly evolving. For the halophyte Oryza coarctata, we found that despite detection of gene fractionation in the subgenomes, homoeologous genes were expressed at higher levels in one subgenome over the other in a mosaic form, demonstrating subgenome equivalence. The integration of these 11 new reference genomes with previously published genome datasets provides a nearly complete view of the consequences of evolution for genome diversification across the genus.
Authors
- Saule Mussurova (ORCID: https://orcid.org/0009-0006-9454-0463)
- Praveena Parakkal
- Rod A. Wing (ORCID: https://orcid.org/0000-0001-6633-6226)
- M. Eric Schranz (ORCID: https://orcid.org/0000-0001-6777-6565)
- Shanmugam Rajasekar (ORCID: https://orcid.org/0000-0001-9038-5618)
- Yong Zhou (ORCID: https://orcid.org/0000-0002-1662-9589)
- Olivier Panaud (ORCID: https://orcid.org/0000-0002-9292-503X)
- Jayson Talag (ORCID: https://orcid.org/0000-0001-6085-214X)
- Manjula Thimma (ORCID: https://orcid.org/0000-0002-1703-8780)
- Andrea Zuccolo (ORCID: https://orcid.org/0000-0001-7574-0714)
- David Kudrna (ORCID: https://orcid.org/0000-0002-3092-3629)
- Luis F. Rivera (ORCID: https://orcid.org/0000-0003-3978-7640)
- Nam V. Hoang (ORCID: https://orcid.org/0000-0003-0782-2835)
- Nahed Mohammed (ORCID: https://orcid.org/0000-0002-8857-3246)
- Noor Al-Bader (ORCID: https://orcid.org/0000-0002-0511-6972)
- Gopal Misra
- Aseel Alsantely (ORCID: https://orcid.org/0000-0002-4990-249X)
- Dario Copetti (ORCID: https://orcid.org/0000-0002-2680-2568)
- Tao Feng (ORCID: https://orcid.org/0000-0002-0489-2021)
- Chandler Sobel-Sorenson
- Marie‐Christine Carpentier (ORCID: https://orcid.org/0000-0002-4795-9054)
- Víctor Llaca (ORCID: https://orcid.org/0000-0003-4822-2924)
- Alice Fornasiero (ORCID: https://orcid.org/0000-0001-6165-4233)
- Leonardo Fabbian (ORCID: https://orcid.org/0009-0001-1475-6576)
- Jianwei Zhang (ORCID: https://orcid.org/0000-0001-8030-5346)
- Seunghee Lee (ORCID: https://orcid.org/0000-0001-8404-6150)
- Millicent D. Alexandrov Sanciangco (ORCID: https://orcid.org/0000-0002-9613-5537)
Institutions
- Centre National de la Recherche Scientifique (FR)
- University of Arizona (US)
- Université de Perpignan (FR)
- International Rice Research Institute (PH)
- Scuola Superiore Sant'Anna (IT)
- Huazhong Agricultural University (CN)
- Saudi Heart Association (SA)
- Corteva (United States) (US)
- Laboratoire Génome et Développement des Plantes (FR)
- Institut de Recherche pour le Développement (FR)
- King Abdullah University of Science and Technology (SA)
- Wageningen University & Research (NL)
Publication Details
- Journal
- Nature Genetics
- Published
- 2025-04-28
- DOI
- https://doi.org/10.1038/s41588-025-02183-5
- Citations
- 15
- Primary Topic
- Genomics and Phylogenetic Studies
- Type
- article
- Field-Weighted Citation Impact
- 12.09
Funders
- Nederlandse Organisatie voor Wetenschappelijk Onderzoek
- King Abdullah University of Science and Technology