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Genomes of 13 Domesticated and Wild Rice Relatives Highlight Genetic Conservation, Turnover and Innovation Across the Genus Oryza
Joshua C. Stein, Yeisoo Yu, Dario Copetti, Derrick J. Zwickl, Li Zhang, Chengjun Zhang, Kapeel Chougule, Dongying Gao, Aiko Iwata, Jose Luis Goicoechea, Sharon Wei, Jun Wang, Yi Liao…Thomas Wicker, Mingsheng Chen, Bin Han, Robert Henry, Yue-ie C. Hsing, Nori Kurata, Antonio Costa de Oliveira, Olivier Panaud, Scott A. Jackson, Carlos A. Machado, Michael J. Sanderson, Manyuan Long, Doreen Ware and Rod A. Wing.
Nature Genetics
Abstract
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.
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DOI:10.1038/s41588-018-0040-0 |
论文题目: |
Genomes of 13 Domesticated and Wild Rice Relatives Highlight Genetic Conservation, Turnover and Innovation Across the Genus Oryza |
英文论文题目: |
Genomes of 13 Domesticated and Wild Rice Relatives Highlight Genetic Conservation, Turnover and Innovation Across the Genus Oryza |
第一作者: |
Joshua C. Stein, Yeisoo Yu, Dario Copetti, Derrick J. Zwickl, Li Zhang, Chengjun Zhang, Kapeel Chougule, Dongying Gao, Aiko Iwata, Jose Luis Goicoechea, Sharon Wei, Jun Wang, Yi Liao…Thomas Wicker, Mingsheng Chen, Bin Han, Robert Henry, Yue-ie C. Hsing, Nori Kurata, Antonio Costa de Oliveira, Olivier Panaud, Scott A. Jackson, Carlos A. Machado, Michael J. Sanderson, Manyuan Long, Doreen Ware and Rod A. Wing. |
英文第一作者: |
Joshua C. Stein, Yeisoo Yu, Dario Copetti, Derrick J. Zwickl, Li Zhang, Chengjun Zhang, Kapeel Chougule, Dongying Gao, Aiko Iwata, Jose Luis Goicoechea, Sharon Wei, Jun Wang, Yi Liao…Thomas Wicker, Mingsheng Chen, Bin Han, Robert Henry, Yue-ie C. Hsing, Nori Kurata, Antonio Costa de Oliveira, Olivier Panaud, Scott A. Jackson, Carlos A. Machado, Michael J. Sanderson, Manyuan Long, Doreen Ware and Rod A. Wing. |
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2018-01-25 |
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摘要: |
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. |
英文摘要: |
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. |
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Nature Genetics |
英文刊物名称: |
Nature Genetics |
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其它备注: |
Joshua C. Stein, Yeisoo Yu, Dario Copetti, Derrick J. Zwickl, Li Zhang, Chengjun Zhang, Kapeel Chougule, Dongying Gao, Aiko Iwata, Jose Luis Goicoechea, Sharon Wei, Jun Wang, Yi Liao…Thomas Wicker, Mingsheng Chen, Bin Han, Robert Henry, Yue-ie C. Hsing, Nori Kurata, Antonio Costa de Oliveira, Olivier Panaud, Scott A. Jackson, Carlos A. Machado, Michael J. Sanderson, Manyuan Long, Doreen Ware and Rod A. Wing. Genomes of 13 Domesticated and Wild Rice Relatives Highlight Genetic Conservation, Turnover and Innovation Across the Genus Oryza. Nature Genetics DOI:10.1038/s41588-018-0040-0 |
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