Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza
The genus Oryza is a model system for the study of molecular evolution over time scales ranging from a few thousand to 15 million years. Using 13 reference genomes spanning the Oryza species tree, we show that despite few large-scale chromosomal rearrangements rapid species diversification is mirror...
| Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Springer
2018
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| Acceso en línea: | https://hdl.handle.net/10568/164912 |
| _version_ | 1855516952747835392 |
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| author | Stein, Joshua C. Yu, Yeisoo Copetti, Dario Zwickl, Derrick J. Zhang, Li Zhang, Chengjun Chougule, Kapeel Gao, Dongying Iwata, Aiko Goicoechea, Jose Luis Wei, Sharon Wang, Jun Liao, Yi Wang, Muhua Jacquemin, Julie Becker, Claude Kudrna, Dave Zhang, Jianwei Londono, Carlos E. M. Song, Xiang Lee, Seunghee Sanchez, Paul Zuccolo, Andrea Ammiraju, Jetty S. S. Talag, Jayson Danowitz, Ann Rivera, Luis F. Gschwend, Andrea R. Noutsos, Christos Wu, Cheng-chieh Kao, Shu-Min Zeng, Jhih-wun Wei, Fu-Jin Zhao, Qiang Feng, Qi El Baidouri, Moaine Carpentier, Marie-Christine Lasserre, Eric Cooke, Richard Rosa Farias, Daniel da da Maia, Luciano Carlos dos Santos, Railson S. Nyberg, Kevin G. McNally, Kenneth L. Mauleon, Ramil Alexandrov, Nickolai Schmutz, Jeremy Flowers, Dave Fan, Chuanzhu Weigel, Detlef Jena, Kshirod K. Wicker, Thomas Chen, Mingsheng Han, Bin Henry, Robert Hsing, Yue-ie C. Kurata, Nori de Oliveira, Antonio Costa Panaud, Olivier Jackson, Scott A. Machado, Carlos A. Sanderson, Michael J. Long, Manyuan Ware, Doreen Wing, Rod A. |
| author_browse | Alexandrov, Nickolai Ammiraju, Jetty S. S. Becker, Claude Carpentier, Marie-Christine Chen, Mingsheng Chougule, Kapeel Cooke, Richard Copetti, Dario Danowitz, Ann El Baidouri, Moaine Fan, Chuanzhu Feng, Qi Flowers, Dave Gao, Dongying Goicoechea, Jose Luis Gschwend, Andrea R. Han, Bin Henry, Robert Hsing, Yue-ie C. Iwata, Aiko Jackson, Scott A. Jacquemin, Julie Jena, Kshirod K. Kao, Shu-Min Kudrna, Dave Kurata, Nori Lasserre, Eric Lee, Seunghee Liao, Yi Londono, Carlos E. M. Long, Manyuan Machado, Carlos A. Mauleon, Ramil McNally, Kenneth L. Noutsos, Christos Nyberg, Kevin G. Panaud, Olivier Rivera, Luis F. Rosa Farias, Daniel da Sanchez, Paul Sanderson, Michael J. Schmutz, Jeremy Song, Xiang Stein, Joshua C. Talag, Jayson Wang, Jun Wang, Muhua Ware, Doreen Wei, Fu-Jin Wei, Sharon Weigel, Detlef Wicker, Thomas Wing, Rod A. Wu, Cheng-chieh Yu, Yeisoo Zeng, Jhih-wun Zhang, Chengjun Zhang, Jianwei Zhang, Li Zhao, Qiang Zuccolo, Andrea Zwickl, Derrick J. da Maia, Luciano Carlos de Oliveira, Antonio Costa dos Santos, Railson S. |
| author_facet | Stein, Joshua C. Yu, Yeisoo Copetti, Dario Zwickl, Derrick J. Zhang, Li Zhang, Chengjun Chougule, Kapeel Gao, Dongying Iwata, Aiko Goicoechea, Jose Luis Wei, Sharon Wang, Jun Liao, Yi Wang, Muhua Jacquemin, Julie Becker, Claude Kudrna, Dave Zhang, Jianwei Londono, Carlos E. M. Song, Xiang Lee, Seunghee Sanchez, Paul Zuccolo, Andrea Ammiraju, Jetty S. S. Talag, Jayson Danowitz, Ann Rivera, Luis F. Gschwend, Andrea R. Noutsos, Christos Wu, Cheng-chieh Kao, Shu-Min Zeng, Jhih-wun Wei, Fu-Jin Zhao, Qiang Feng, Qi El Baidouri, Moaine Carpentier, Marie-Christine Lasserre, Eric Cooke, Richard Rosa Farias, Daniel da da Maia, Luciano Carlos dos Santos, Railson S. Nyberg, Kevin G. McNally, Kenneth L. Mauleon, Ramil Alexandrov, Nickolai Schmutz, Jeremy Flowers, Dave Fan, Chuanzhu Weigel, Detlef Jena, Kshirod K. Wicker, Thomas Chen, Mingsheng Han, Bin Henry, Robert Hsing, Yue-ie C. Kurata, Nori de Oliveira, Antonio Costa Panaud, Olivier Jackson, Scott A. Machado, Carlos A. Sanderson, Michael J. Long, Manyuan Ware, Doreen Wing, Rod A. |
| author_sort | Stein, Joshua C. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | The genus Oryza is a model system for the study of molecular evolution over time scales ranging from a few thousand to 15 million years. Using 13 reference genomes spanning the Oryza species tree, we show that despite few large-scale chromosomal rearrangements rapid species diversification is mirrored by lineage-specific emergence and turnover of many novel elements, including transposons, and potential new coding and noncoding genes. Our study resolves controversial areas of the Oryza phylogeny, showing a complex history of introgression among different chromosomes in the young ‘AA’ subclade containing the two domesticated species. This study highlights the prevalence of functionally coupled disease resistance genes and identifies many new haplotypes of potential use for future crop protection. Finally, this study marks a milestone in modern rice research with the release of a complete long-read assembly of IR 8 ‘Miracle Rice’, which relieved famine and drove the Green Revolution in Asia 50 years ago |
| format | Journal Article |
| id | CGSpace164912 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2018 |
| publishDateRange | 2018 |
| publishDateSort | 2018 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | CGSpace1649122025-05-14T10:23:54Z Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza Stein, Joshua C. Yu, Yeisoo Copetti, Dario Zwickl, Derrick J. Zhang, Li Zhang, Chengjun Chougule, Kapeel Gao, Dongying Iwata, Aiko Goicoechea, Jose Luis Wei, Sharon Wang, Jun Liao, Yi Wang, Muhua Jacquemin, Julie Becker, Claude Kudrna, Dave Zhang, Jianwei Londono, Carlos E. M. Song, Xiang Lee, Seunghee Sanchez, Paul Zuccolo, Andrea Ammiraju, Jetty S. S. Talag, Jayson Danowitz, Ann Rivera, Luis F. Gschwend, Andrea R. Noutsos, Christos Wu, Cheng-chieh Kao, Shu-Min Zeng, Jhih-wun Wei, Fu-Jin Zhao, Qiang Feng, Qi El Baidouri, Moaine Carpentier, Marie-Christine Lasserre, Eric Cooke, Richard Rosa Farias, Daniel da da Maia, Luciano Carlos dos Santos, Railson S. Nyberg, Kevin G. McNally, Kenneth L. Mauleon, Ramil Alexandrov, Nickolai Schmutz, Jeremy Flowers, Dave Fan, Chuanzhu Weigel, Detlef Jena, Kshirod K. Wicker, Thomas Chen, Mingsheng Han, Bin Henry, Robert Hsing, Yue-ie C. Kurata, Nori de Oliveira, Antonio Costa Panaud, Olivier Jackson, Scott A. Machado, Carlos A. Sanderson, Michael J. Long, Manyuan Ware, Doreen Wing, Rod A. The genus Oryza is a model system for the study of molecular evolution over time scales ranging from a few thousand to 15 million years. Using 13 reference genomes spanning the Oryza species tree, we show that despite few large-scale chromosomal rearrangements rapid species diversification is mirrored by lineage-specific emergence and turnover of many novel elements, including transposons, and potential new coding and noncoding genes. Our study resolves controversial areas of the Oryza phylogeny, showing a complex history of introgression among different chromosomes in the young ‘AA’ subclade containing the two domesticated species. This study highlights the prevalence of functionally coupled disease resistance genes and identifies many new haplotypes of potential use for future crop protection. Finally, this study marks a milestone in modern rice research with the release of a complete long-read assembly of IR 8 ‘Miracle Rice’, which relieved famine and drove the Green Revolution in Asia 50 years ago 2018-02 2024-12-19T12:54:27Z 2024-12-19T12:54:27Z Journal Article https://hdl.handle.net/10568/164912 en Open Access Springer Stein, Joshua C.; Yu, Yeisoo; Copetti, Dario; Zwickl, Derrick J.; Zhang, Li; Zhang, Chengjun; Chougule, Kapeel; Gao, Dongying; Iwata, Aiko; Goicoechea, Jose Luis; Wei, Sharon; Wang, Jun; Liao, Yi; Wang, Muhua; Jacquemin, Julie; Becker, Claude; Kudrna, Dave; Zhang, Jianwei; Londono, Carlos E. M.; Song, Xiang; Lee, Seunghee; Sanchez, Paul; Zuccolo, Andrea; Ammiraju, Jetty S. S.; Talag, Jayson; Danowitz, Ann; Rivera, Luis F.; Gschwend, Andrea R.; Noutsos, Christos; Wu, Cheng-chieh; Kao, Shu-min; Zeng, Jhih-wun; Wei, Fu-jin; Zhao, Qiang; Feng, Qi; El Baidouri, Moaine; Carpentier, Marie-Christine; Lasserre, Eric; Cooke, Richard; Rosa Farias, Daniel da; da Maia, Luciano Carlos; dos Santos, Railson S.; Nyberg, Kevin G.; McNally, Kenneth L.; Mauleon, Ramil; Alexandrov, Nickolai; Schmutz, Jeremy; Flowers, Dave; Fan, Chuanzhu; Weigel, Detlef; Jena, Kshirod K.; Wicker, Thomas; Chen, Mingsheng; Han, Bin; Henry, Robert; Hsing, Yue-ie C.; Kurata, Nori; de Oliveira, Antonio Costa; Panaud, Olivier; Jackson, Scott A.; Machado, Carlos A.; Sanderson, Michael J.; Long, Manyuan; Ware, Doreen and Wing, Rod A. 2018. Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza. Nat Genet, Volume 50 no. 2 p. 285-296 |
| spellingShingle | Stein, Joshua C. Yu, Yeisoo Copetti, Dario Zwickl, Derrick J. Zhang, Li Zhang, Chengjun Chougule, Kapeel Gao, Dongying Iwata, Aiko Goicoechea, Jose Luis Wei, Sharon Wang, Jun Liao, Yi Wang, Muhua Jacquemin, Julie Becker, Claude Kudrna, Dave Zhang, Jianwei Londono, Carlos E. M. Song, Xiang Lee, Seunghee Sanchez, Paul Zuccolo, Andrea Ammiraju, Jetty S. S. Talag, Jayson Danowitz, Ann Rivera, Luis F. Gschwend, Andrea R. Noutsos, Christos Wu, Cheng-chieh Kao, Shu-Min Zeng, Jhih-wun Wei, Fu-Jin Zhao, Qiang Feng, Qi El Baidouri, Moaine Carpentier, Marie-Christine Lasserre, Eric Cooke, Richard Rosa Farias, Daniel da da Maia, Luciano Carlos dos Santos, Railson S. Nyberg, Kevin G. McNally, Kenneth L. Mauleon, Ramil Alexandrov, Nickolai Schmutz, Jeremy Flowers, Dave Fan, Chuanzhu Weigel, Detlef Jena, Kshirod K. Wicker, Thomas Chen, Mingsheng Han, Bin Henry, Robert Hsing, Yue-ie C. Kurata, Nori de Oliveira, Antonio Costa Panaud, Olivier Jackson, Scott A. Machado, Carlos A. Sanderson, Michael J. Long, Manyuan Ware, Doreen Wing, Rod A. Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza |
| title | Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza |
| title_full | Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza |
| title_fullStr | Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza |
| title_full_unstemmed | Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza |
| title_short | Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza |
| title_sort | genomes of 13 domesticated and wild rice relatives highlight genetic conservation turnover and innovation across the genus oryza |
| url | https://hdl.handle.net/10568/164912 |
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