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


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2018-01-22

AUTHORS

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, Dave Kudrna, Jianwei Zhang, Carlos E. M. Londono, Xiang Song, Seunghee 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 J. Sanderson, Manyuan Long, Doreen Ware, Rod A. Wing

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. More... »

PAGES

285-296

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  • Journal

    TITLE

    Nature Genetics

    ISSUE

    2

    VOLUME

    50

    Author Affiliations

  • Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
  • Phyzen Genomics Institute, Phyzen, Inc., Seoul, South Korea
  • International Rice Research Institute, Los Baños, Philippines
  • Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
  • Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
  • Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA
  • Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
  • Department of Biological Sciences, Wayne State University, Detroit, MI, USA
  • State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
  • Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
  • Crop Biodiversity and Breeding Informatics Group, Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Stuttgart, Germany
  • Max Planck Institute for Developmental Biology, Tübingen, Germany
  • Rice Experiment Station, Biggs, CA, USA
  • Institute of Life Sciences, Scuola Superiore Sant’Anna, Pisa, Italy
  • DuPont-Pioneer, Johnston, IA, USA
  • BIOS–Parque Los Yarumos, Manizales, Colombia
  • Institute of Botany, National Taiwan University, Taipei, Taiwan
  • Department of Plant Systems Biology, VIB and Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
  • Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
  • Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Tsukuba, Japan
  • National Center for Gene Research, Chinese Academy of Sciences, Shanghai, China
  • Laboratoire Génome et Développement des Plantes, UMR 5096 UPVD/CNRS, Université de Perpignan Via Domitia, Perpignan, France
  • Plant Genomics and Breeding Center, Universidade Federal de Pelotas, Pelotas, Brazil
  • Department of Biology, University of Maryland, College Park, MD, USA
  • HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
  • Institute of Plant Biology, University of Zurich, Zurich, Switzerland
  • Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Queensland, Australia
  • National Institute of Genetics, Mishima, Japan
  • Robert W. Holley Center for Agriculture and Health, US Department of Agriculture, Agricultural Research Service, Ithaca, NY, USA
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/s41588-018-0040-0

    DOI

    http://dx.doi.org/10.1038/s41588-018-0040-0

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1100426990

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/29358651


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    56 schema: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.
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