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

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.

Authors:
 [1];  [2];  [3];  [4]; ORCiD logo [5]; ORCiD logo [5];  [6];  [7];  [7];  [4];  [1];  [8];  [9];  [10];  [11]; ORCiD logo [12];  [4];  [4];  [4];  [4] more »;  [4];  [13]; ORCiD logo [14];  [15];  [4];  [4];  [16];  [5];  [1];  [17];  [18];  [19];  [20];  [21]; ORCiD logo [21];  [22];  [22]; ORCiD logo [22];  [22];  [23];  [23];  [23];  [24];  [25];  [25];  [25];  [26];  [26];  [8];  [12];  [25];  [27];  [9];  [21]; ORCiD logo [28];  [19];  [29];  [23]; ORCiD logo [22]; ORCiD logo [7];  [24];  [4]; ORCiD logo [5]; ORCiD logo [30]; ORCiD logo [3] « less
  1. Cold Spring Harbor Lab., NY (United States)
  2. Univ. of Arizona, Tucson, AZ (United States); Phyzen, Inc., Seoul (South Korea)
  3. Univ. of Arizona, Tucson, AZ (United States); International Rice Research Inst., Los Baños (Philippines)
  4. Univ. of Arizona, Tucson, AZ (United States)
  5. Univ. of Chicago, IL (United States)
  6. Cold Spring Harbor Lab., NY (United States); Univ. of Arizona, Tucson, AZ (United States)
  7. Univ. of Georgia, Athens, GA (United States)
  8. Wayne State Univ., Detroit, MI (United States)
  9. Chinese Academy of Sciences (CAS), Beijing (China)
  10. Univ. of Arizona, Tucson, AZ (United States); Friedrich Miescher Lab. of the Max Planck Society, Tübingen (Germany)
  11. Univ. of Arizona, Tucson, AZ (United States); Univ. of Hohenheim, Stuttgart (Germany)
  12. Max Planck Inst. for Developmental Biology, Tübingen (Germany)
  13. Univ. of Arizona, Tucson, AZ (United States); Rice Experiment Station, Biggs, CA (United States)
  14. Univ. of Arizona, Tucson, AZ (United States); Sant'Anna School of Advanced Studies, Pisa (Italy)
  15. Univ. of Arizona, Tucson, AZ (United States); DuPont-Pioneer, Johnston, IA (United States)
  16. Univ. of Arizona, Tucson, AZ (United States); BIOS-Parque Los Yarumos, Manizales (Colombia)
  17. Academia Sinica, Taipei (Taiwan); National Taiwan Univ., Taipei (Taiwan)
  18. Academia Sinica, Taipei (Taiwan); Ghent Univ. (Belgium)
  19. Academia Sinica, Taipei (Taiwan)
  20. Academia Sinica, Taipei (Taiwan); Forestry and Forest Products Research Inst., Tsukuba (Japan)
  21. Chinese Academy of Sciences (CAS), Shanghai (China)
  22. Univ. of Perpignan-Domitian (France)
  23. Federal Univ. of Pelotas (Brazil)
  24. Univ. of Maryland, College Park, MD (United States)
  25. International Rice Research Inst., Los Baños (Philippines)
  26. HudsonAlpha Inst. for Biotechnology, Huntsville, AL (United States)
  27. Univ. of Zurich (Switzerland)
  28. Univ. of Queensland, Brisbane (Australia)
  29. National Inst. of Genetics, Mishima (Japan)
  30. Cold Spring Harbor Lab., NY (United States); US Dept. of Agriculture-Agricultural Research Service (USDA-ARS), Ithaca, NY (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER); National Science Foundation (NSF)
OSTI Identifier:
1543774
Alternate Identifier(s):
OSTI ID: 1616059
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Nature Genetics
Additional Journal Information:
Journal Volume: 50; Journal Issue: 2; Journal ID: ISSN 1061-4036
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

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. Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza. United States: N. p., 2018. Web. doi: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, 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. United States. 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, 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. Mon . "Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza". United States. https://doi.org/10.1038/s41588-018-0040-0. https://www.osti.gov/servlets/purl/1543774.
@article{osti_1543774,
title = {Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza},
author = {Stein, Joshua C. and Yu, Yeisoo and Copetti, Dario and Zwickl, Derrick J. and Zhang, Li and Zhang, Chengjun and Chougule, Kapeel and Gao, Dongying and Iwata, Aiko and Goicoechea, Jose Luis and Wei, Sharon and Wang, Jun and Liao, Yi and Wang, Muhua and Jacquemin, Julie and Becker, Claude and Kudrna, Dave and Zhang, Jianwei and Londono, Carlos E. M. and Song, Xiang and Lee, Seunghee and Sanchez, Paul and Zuccolo, Andrea and Ammiraju, Jetty S. S. and Talag, Jayson and Danowitz, Ann and Rivera, Luis F. and Gschwend, Andrea R. and Noutsos, Christos and Wu, Cheng-chieh and Kao, Shu-min and Zeng, Jhih-wun and Wei, Fu-jin and Zhao, Qiang and Feng, Qi and El Baidouri, Moaine and Carpentier, Marie-Christine and Lasserre, Eric and Cooke, Richard and Rosa Farias, Daniel da and da Maia, Luciano Carlos and dos Santos, Railson S. and Nyberg, Kevin G. and McNally, Kenneth L. and Mauleon, Ramil and Alexandrov, Nickolai and Schmutz, Jeremy and Flowers, Dave and Fan, Chuanzhu and Weigel, Detlef and Jena, Kshirod K. and Wicker, Thomas and Chen, Mingsheng and Han, Bin and Henry, Robert and Hsing, Yue-ie C. and Kurata, Nori and de Oliveira, Antonio Costa and Panaud, Olivier and Jackson, Scott A. and Machado, Carlos A. and Sanderson, Michael J. and Long, Manyuan and Ware, Doreen and Wing, Rod A.},
abstractNote = {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.},
doi = {10.1038/s41588-018-0040-0},
journal = {Nature Genetics},
number = 2,
volume = 50,
place = {United States},
year = {Mon Jan 22 00:00:00 EST 2018},
month = {Mon Jan 22 00:00:00 EST 2018}
}

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