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, Muhua Wang, Julie Jacquemin, Claude Becker, David A Kudrna, Jianwei - Zhang, Carlos E.M. Londono, Xiang SongSeunghee Lee, Paul Sanchez, Andrea Zuccolo, Jetty S.S. Ammiraju, Jayson Talag, Ann Danowitz, Luis F. Rivera, Andrea R. Gschwend, Christos Noutsos, Cheng Chieh Wu, Shu Min Kao, Jhih Wun Zeng, Fu Jin Wei, Qiang Zhao, Qi Feng, Moaine El Baidouri, Marie Christine Carpentier, Eric Lasserre, Richard Cooke, Daniel Da Rosa Farias, Luciano Carlos Da Maia, Railson S. Dos Santos, Kevin G. Nyberg, Kenneth L. McNally, Ramil Mauleon, Nickolai Alexandrov, Jeremy Schmutz, Dave Flowers, Chuanzhu Fan, Detlef Weigel, Kshirod K. Jena, 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 Sanderson, Manyuan Long, Doreen Ware, Rod A Wing

Research output: Contribution to journalArticle

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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.

Original languageEnglish (US)
Pages (from-to)285-296
Number of pages12
JournalNature Genetics
Volume50
Issue number2
DOIs
StatePublished - Feb 1 2018

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Genome
Disease Resistance
Molecular Evolution
Phylogeny
Starvation
Haplotypes
Genes
Cross-Sectional Studies
Chromosomes
Oryza
Research

ASJC Scopus subject areas

  • Genetics

Cite this

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, David A; 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; Long, Manyuan; Ware, Doreen; Wing, Rod A.

In: Nature Genetics, Vol. 50, No. 2, 01.02.2018, p. 285-296.

Research output: Contribution to journalArticle

Stein, JC, Yu, Y, Copetti, D, Zwickl, DJ, Zhang, L, Zhang, C, Chougule, K, Gao, D, Iwata, A, Goicoechea, JL, Wei, S, Wang, J, Liao, Y, Wang, M, Jacquemin, J, Becker, C, Kudrna, DA, Zhang, J, Londono, CEM, Song, X, Lee, S, Sanchez, P, Zuccolo, A, Ammiraju, JSS, Talag, J, Danowitz, A, Rivera, LF, Gschwend, AR, Noutsos, C, Wu, CC, Kao, SM, Zeng, JW, Wei, FJ, Zhao, Q, Feng, Q, El Baidouri, M, Carpentier, MC, Lasserre, E, Cooke, R, Rosa Farias, DD, Da Maia, LC, Dos Santos, RS, Nyberg, KG, McNally, KL, Mauleon, R, Alexandrov, N, Schmutz, J, Flowers, D, Fan, C, Weigel, D, Jena, KK, Wicker, T, Chen, M, Han, B, Henry, R, Hsing, YIC, Kurata, N, De Oliveira, AC, Panaud, O, Jackson, SA, Machado, CA, Sanderson, M, Long, M, Ware, D & Wing, RA 2018, 'Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza', Nature Genetics, vol. 50, no. 2, pp. 285-296. https://doi.org/10.1038/s41588-018-0040-0
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, David A ; 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 ; 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. In: Nature Genetics. 2018 ; Vol. 50, No. 2. pp. 285-296.
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