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. 2018 Feb;50(2):285-296.
doi: 10.1038/s41588-018-0040-0. Epub 2018 Jan 22.

Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

Joshua C Stein  1 , Yeisoo Yu  2   3 , Dario Copetti  2   4 , Derrick J Zwickl  5 , Li Zhang  6 , Chengjun Zhang  6 , Kapeel Chougule  1   2 , Dongying Gao  7 , Aiko Iwata  7 , Jose Luis Goicoechea  2 , Sharon Wei  1 , Jun Wang  8 , Yi Liao  9 , Muhua Wang  2   10 , Julie Jacquemin  2   11 , Claude Becker  12 , Dave Kudrna  2 , Jianwei Zhang  2 , Carlos E M Londono  2 , Xiang Song  2 , Seunghee Lee  2 , Paul Sanchez  2   13 , Andrea Zuccolo  2   14 , Jetty S S Ammiraju  2   15 , Jayson Talag  2 , Ann Danowitz  2 , Luis F Rivera  2   16 , Andrea R Gschwend  6 , Christos Noutsos  1 , Cheng-Chieh Wu  17   18 , Shu-Min Kao  17   19 , Jhih-Wun Zeng  17 , Fu-Jin Wei  17   20 , Qiang Zhao  21 , Qi Feng  21 , Moaine El Baidouri  22 , Marie-Christine Carpentier  22 , Eric Lasserre  22 , Richard Cooke  22 , Daniel da Rosa Farias  23 , Luciano Carlos da Maia  23 , Railson S Dos Santos  23 , Kevin G Nyberg  24 , Kenneth L McNally  4 , Ramil Mauleon  4 , Nickolai Alexandrov  4 , Jeremy Schmutz  25 , Dave Flowers  25 , Chuanzhu Fan  8 , Detlef Weigel  12 , Kshirod K Jena  4 , Thomas Wicker  26 , Mingsheng Chen  9 , Bin Han  21 , Robert Henry  27 , Yue-Ie C Hsing  17 , Nori Kurata  28 , Antonio Costa de Oliveira  23 , Olivier Panaud  22 , Scott A Jackson  7 , Carlos A Machado  24 , Michael J Sanderson  5 , Manyuan Long  6 , Doreen Ware  1   29 , Rod A Wing  30   31   32
Affiliations
Free article

Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

Joshua C Stein et al. Nat Genet. 2018 Feb.
Free article

Erratum in

  • Publisher Correction: Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza.
    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 D, 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, da Rosa Farias D, 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 YC, Kurata N, de Oliveira AC, Panaud O, Jackson SA, Machado CA, Sanderson MJ, Long M, Ware D, Wing RA. Stein JC, et al. Nat Genet. 2018 Nov;50(11):1618. doi: 10.1038/s41588-018-0261-2. Nat Genet. 2018. PMID: 30291357

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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