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...
| Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Springer
2025
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/175744 |
| _version_ | 1855538718683693056 |
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| author | Fornasiero, Alice Feng, Tao Al-Bader, Noor Alsantely, Aseel Mussurova, Saule Hoang, Nam V. Misra, Gopal Zhou, Yong Fabbian, Leonardo Mohammed, Nahed Rivera Serna, Luis Thimma, Manjula Llaca, Victor Parakkal, Praveena Kudrna, David Copetti, Dario Rajasekar, Shanmugam Lee, Seunghee Talag, Jayson Sobel-Sorenson, Chandler Carpentier, Marie-Christine Panaud, Olivier McNally, Kenneth L. Zhang, Jianwei Zuccolo, Andrea Schranz, M. Eric Wing, Rod A. |
| author_browse | Al-Bader, Noor Alsantely, Aseel Carpentier, Marie-Christine Copetti, Dario Fabbian, Leonardo Feng, Tao Fornasiero, Alice Hoang, Nam V. Kudrna, David Lee, Seunghee Llaca, Victor McNally, Kenneth L. Misra, Gopal Mohammed, Nahed Mussurova, Saule Panaud, Olivier Parakkal, Praveena Rajasekar, Shanmugam Rivera Serna, Luis Schranz, M. Eric Sobel-Sorenson, Chandler Talag, Jayson Thimma, Manjula Wing, Rod A. Zhang, Jianwei Zhou, Yong Zuccolo, Andrea |
| author_facet | Fornasiero, Alice Feng, Tao Al-Bader, Noor Alsantely, Aseel Mussurova, Saule Hoang, Nam V. Misra, Gopal Zhou, Yong Fabbian, Leonardo Mohammed, Nahed Rivera Serna, Luis Thimma, Manjula Llaca, Victor Parakkal, Praveena Kudrna, David Copetti, Dario Rajasekar, Shanmugam Lee, Seunghee Talag, Jayson Sobel-Sorenson, Chandler Carpentier, Marie-Christine Panaud, Olivier McNally, Kenneth L. Zhang, Jianwei Zuccolo, Andrea Schranz, M. Eric Wing, Rod A. |
| author_sort | Fornasiero, Alice |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | 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. |
| format | Journal Article |
| id | CGSpace175744 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2025 |
| publishDateRange | 2025 |
| publishDateSort | 2025 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | CGSpace1757442025-12-08T10:06:44Z Oryza genome evolution through a tetraploid lens Fornasiero, Alice Feng, Tao Al-Bader, Noor Alsantely, Aseel Mussurova, Saule Hoang, Nam V. Misra, Gopal Zhou, Yong Fabbian, Leonardo Mohammed, Nahed Rivera Serna, Luis Thimma, Manjula Llaca, Victor Parakkal, Praveena Kudrna, David Copetti, Dario Rajasekar, Shanmugam Lee, Seunghee Talag, Jayson Sobel-Sorenson, Chandler Carpentier, Marie-Christine Panaud, Olivier McNally, Kenneth L. Zhang, Jianwei Zuccolo, Andrea Schranz, M. Eric Wing, Rod A. genomes chromosome mapping Oryza gene expression gene pools crop improvement plant breeding evolution genetic resources haplotypes genetic variation domestication 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. 2025-05 2025-07-23T05:59:16Z 2025-07-23T05:59:16Z Journal Article https://hdl.handle.net/10568/175744 en Open Access application/pdf Springer Fornasiero, Alice, Tao Feng, Noor Al-Bader, Aseel Alsantely, Saule Mussurova, Nam V. Hoang, Gopal Misra et al. "Oryza genome evolution through a tetraploid lens." Nature Genetics 57, no. 5 (2025): 1287-1297. |
| spellingShingle | genomes chromosome mapping Oryza gene expression gene pools crop improvement plant breeding evolution genetic resources haplotypes genetic variation domestication Fornasiero, Alice Feng, Tao Al-Bader, Noor Alsantely, Aseel Mussurova, Saule Hoang, Nam V. Misra, Gopal Zhou, Yong Fabbian, Leonardo Mohammed, Nahed Rivera Serna, Luis Thimma, Manjula Llaca, Victor Parakkal, Praveena Kudrna, David Copetti, Dario Rajasekar, Shanmugam Lee, Seunghee Talag, Jayson Sobel-Sorenson, Chandler Carpentier, Marie-Christine Panaud, Olivier McNally, Kenneth L. Zhang, Jianwei Zuccolo, Andrea Schranz, M. Eric Wing, Rod A. Oryza genome evolution through a tetraploid lens |
| title | Oryza genome evolution through a tetraploid lens |
| title_full | Oryza genome evolution through a tetraploid lens |
| title_fullStr | Oryza genome evolution through a tetraploid lens |
| title_full_unstemmed | Oryza genome evolution through a tetraploid lens |
| title_short | Oryza genome evolution through a tetraploid lens |
| title_sort | oryza genome evolution through a tetraploid lens |
| topic | genomes chromosome mapping Oryza gene expression gene pools crop improvement plant breeding evolution genetic resources haplotypes genetic variation domestication |
| url | https://hdl.handle.net/10568/175744 |
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