Genome sequence of the progenitor of the wheat D genome Aegilops tauschii.
Luo MCDepartment of Plant Sciences, University of California, Davis, California, USA.
Gu YQCrop Improvement & Genetics Research, USDA-ARS, Albany, California USA.
Puiu DCenter for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
Wang HInstitute of Plant Breeding, Genetics and Genomics, Department of Crop & Soil Sciences, University of Georgia, Athens, Georgia, USA.
Twardziok SOPlant Genome and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany.
Deal KRDepartment of Plant Sciences, University of California, Davis, California, USA.
Huo NDepartment of Plant Sciences, University of California, Davis, California, USA.
Zhu TDepartment of Plant Sciences, University of California, Davis, California, USA.
Wang LDepartment of Plant Sciences, University of California, Davis, California, USA.
Wang YDepartment of Plant Sciences, University of California, Davis, California, USA.
McGuire PEDepartment of Plant Sciences, University of California, Davis, California, USA.
Liu SDepartment of Plant Sciences, University of California, Davis, California, USA.
Long HDepartment of Plant Sciences, University of California, Davis, California, USA.
Ramasamy RKDepartment of Plant Sciences, University of California, Davis, California, USA.
Rodriguez JCDepartment of Plant Sciences, University of California, Davis, California, USA.
Van SLDepartment of Plant Sciences, University of California, Davis, California, USA.
Yuan LDepartment of Plant Sciences, University of California, Davis, California, USA.
Wang ZDepartment of Plant Sciences, University of California, Davis, California, USA.
Xia ZDepartment of Plant Sciences, University of California, Davis, California, USA.
Xiao LDepartment of Plant Sciences, University of California, Davis, California, USA.
Anderson ODCrop Improvement & Genetics Research, USDA-ARS, Albany, California USA.
Ouyang SCrop Improvement & Genetics Research, USDA-ARS, Albany, California USA.
Liang YCrop Improvement & Genetics Research, USDA-ARS, Albany, California USA.
Zimin AVCenter for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
Pertea GCenter for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
Qi PInstitute of Plant Breeding, Genetics and Genomics, Department of Crop & Soil Sciences, University of Georgia, Athens, Georgia, USA.
Bennetzen JLDepartment of Genetics, University of Georgia, Athens, Georgia, USA.
Dai XDepartment of Statistics, University of California, Davis, California, USA.
Dawson MWDepartment of Statistics, University of California, Davis, California, USA.
Müller HGDepartment of Statistics, University of California, Davis, California, USA.
Kugler KPlant Genome and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany.
Rivarola-Duarte LPlant Genome and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany.
Spannagl MPlant Genome and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany.
Mayer KFXPlant Genome and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany.
Lu FHDepartment Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, UK.
Bevan MWDepartment Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, UK.
Leroy PINRA, UBP, UMR 1095, GDEC, Clermont-Ferrand, France.
Li PAgriculture & Agri-Food Canada, Morden, Winnipeg, Canada.
You FMAgriculture & Agri-Food Canada, Morden, Winnipeg, Canada.
Sun QChina Agricultural University, Beijing, China.
Liu ZChina Agricultural University, Beijing, China.
Lyons ECyVerse, University of Arizona, Tucson, Arizona, USA.
Wicker TDepartment of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland.
Salzberg SLCenter for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
Devos KMInstitute of Plant Breeding, Genetics and Genomics, Department of Crop & Soil Sciences, University of Georgia, Athens, Georgia, USA.
Dvořák JDepartment of Plant Sciences, University of California, Davis, California, USA.
English
Aegilops tauschii is the diploid progenitor of the D genome of hexaploid wheat (Triticum aestivum, genomes AABBDD) and an important genetic resource for wheat. The large size and highly repetitive nature of the Ae. tauschii genome has until now precluded the development of a reference-quality genome sequence. Here we use an array of advanced technologies, including ordered-clone genome sequencing, whole-genome shotgun sequencing, and BioNano optical genome mapping, to generate a reference-quality genome sequence for Ae. tauschii ssp. strangulata accession AL8/78, which is closely related to the wheat D genome. We show that compared to other sequenced plant genomes, including a much larger conifer genome, the Ae. tauschii genome contains unprecedented amounts of very similar repeated sequences. Our genome comparisons reveal that the Ae. tauschii genome has a greater number of dispersed duplicated genes than other sequenced genomes and its chromosomes have been structurally evolving an order of magnitude faster than those of other grass genomes. The decay of colinearity with other grass genomes correlates with recombination rates along chromosomes. We propose that the vast amounts of very similar repeated sequences cause frequent errors in recombination and lead to gene duplications and structural chromosome changes that drive fast genome evolution.