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Genome sequence of the progenitor of the wheat D genome Aegilops tauschii.
Nature. 2017 11 23; 551(7681):498-502.Nat

Abstract

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.

Authors+Show Affiliations

Department of Plant Sciences, University of California, Davis, California, USA.Crop Improvement & Genetics Research, USDA-ARS, Albany, California USA.Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.Institute of Plant Breeding, Genetics and Genomics, Department of Crop & Soil Sciences, University of Georgia, Athens, Georgia, USA. Department of Plant Biology, University of Georgia, Athens, Georgia, USA. Department of Genetics, University of Georgia, Athens, Georgia, USA.Plant Genome and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany.Department of Plant Sciences, University of California, Davis, California, USA.Department of Plant Sciences, University of California, Davis, California, USA. Crop Improvement & Genetics Research, USDA-ARS, Albany, California USA.Department of Plant Sciences, University of California, Davis, California, USA.Department of Plant Sciences, University of California, Davis, California, USA.Department of Plant Sciences, University of California, Davis, California, USA. Crop Improvement & Genetics Research, USDA-ARS, Albany, California USA.Department of Plant Sciences, University of California, Davis, California, USA.Department of Plant Sciences, University of California, Davis, California, USA.Department of Plant Sciences, University of California, Davis, California, USA.Department of Plant Sciences, University of California, Davis, California, USA.Department of Plant Sciences, University of California, Davis, California, USA.Department of Plant Sciences, University of California, Davis, California, USA.Department of Plant Sciences, University of California, Davis, California, USA.Department of Plant Sciences, University of California, Davis, California, USA. China Agricultural University, Beijing, China.Department of Plant Sciences, University of California, Davis, California, USA.Department of Plant Sciences, University of California, Davis, California, USA.Crop Improvement & Genetics Research, USDA-ARS, Albany, California USA.Crop Improvement & Genetics Research, USDA-ARS, Albany, California USA. China Agricultural University, Beijing, China.Crop Improvement & Genetics Research, USDA-ARS, Albany, California USA. China Agricultural University, Beijing, China.Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.Institute of Plant Breeding, Genetics and Genomics, Department of Crop & Soil Sciences, University of Georgia, Athens, Georgia, USA. Department of Plant Biology, University of Georgia, Athens, Georgia, USA.Department of Genetics, University of Georgia, Athens, Georgia, USA.Department of Statistics, University of California, Davis, California, USA.Department of Statistics, University of California, Davis, California, USA.Department of Statistics, University of California, Davis, California, USA.Plant Genome and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany.Plant Genome and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany.Plant Genome and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany.Plant Genome and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany. School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany.Department Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, UK.Department Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, UK.INRA, UBP, UMR 1095, GDEC, Clermont-Ferrand, France.Agriculture & Agri-Food Canada, Morden, Winnipeg, Canada.Agriculture & Agri-Food Canada, Morden, Winnipeg, Canada.China Agricultural University, Beijing, China.China Agricultural University, Beijing, China.CyVerse, University of Arizona, Tucson, Arizona, USA.Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland.Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA. Departments of Biomedical Engineering, Computer Science, and Biostatistics, Johns Hopkins University, Baltimore, Maryland, USA.Institute of Plant Breeding, Genetics and Genomics, Department of Crop & Soil Sciences, University of Georgia, Athens, Georgia, USA. Department of Plant Biology, University of Georgia, Athens, Georgia, USA.Department of Plant Sciences, University of California, Davis, California, USA.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

Language

eng

PubMed ID

29143815

Citation

Luo, Ming-Cheng, et al. "Genome Sequence of the Progenitor of the Wheat D Genome Aegilops Tauschii." Nature, vol. 551, no. 7681, 2017, pp. 498-502.
Luo MC, Gu YQ, Puiu D, et al. Genome sequence of the progenitor of the wheat D genome Aegilops tauschii. Nature. 2017;551(7681):498-502.
Luo, M. C., Gu, Y. Q., Puiu, D., Wang, H., Twardziok, S. O., Deal, K. R., Huo, N., Zhu, T., Wang, L., Wang, Y., McGuire, P. E., Liu, S., Long, H., Ramasamy, R. K., Rodriguez, J. C., Van, S. L., Yuan, L., Wang, Z., Xia, Z., ... Dvořák, J. (2017). Genome sequence of the progenitor of the wheat D genome Aegilops tauschii. Nature, 551(7681), 498-502. https://doi.org/10.1038/nature24486
Luo MC, et al. Genome Sequence of the Progenitor of the Wheat D Genome Aegilops Tauschii. Nature. 2017 11 23;551(7681):498-502. PubMed PMID: 29143815.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Genome sequence of the progenitor of the wheat D genome Aegilops tauschii. AU - Luo,Ming-Cheng, AU - Gu,Yong Q, AU - Puiu,Daniela, AU - Wang,Hao, AU - Twardziok,Sven O, AU - Deal,Karin R, AU - Huo,Naxin, AU - Zhu,Tingting, AU - Wang,Le, AU - Wang,Yi, AU - McGuire,Patrick E, AU - Liu,Shuyang, AU - Long,Hai, AU - Ramasamy,Ramesh K, AU - Rodriguez,Juan C, AU - Van,Sonny L, AU - Yuan,Luxia, AU - Wang,Zhenzhong, AU - Xia,Zhiqiang, AU - Xiao,Lichan, AU - Anderson,Olin D, AU - Ouyang,Shuhong, AU - Liang,Yong, AU - Zimin,Aleksey V, AU - Pertea,Geo, AU - Qi,Peng, AU - Bennetzen,Jeffrey L, AU - Dai,Xiongtao, AU - Dawson,Matthew W, AU - Müller,Hans-Georg, AU - Kugler,Karl, AU - Rivarola-Duarte,Lorena, AU - Spannagl,Manuel, AU - Mayer,Klaus F X, AU - Lu,Fu-Hao, AU - Bevan,Michael W, AU - Leroy,Philippe, AU - Li,Pingchuan, AU - You,Frank M, AU - Sun,Qixin, AU - Liu,Zhiyong, AU - Lyons,Eric, AU - Wicker,Thomas, AU - Salzberg,Steven L, AU - Devos,Katrien M, AU - Dvořák,Jan, Y1 - 2017/11/15/ PY - 2016/09/24/received PY - 2017/10/09/accepted PY - 2017/11/17/pubmed PY - 2018/4/17/medline PY - 2017/11/17/entrez SP - 498 EP - 502 JF - Nature JO - Nature VL - 551 IS - 7681 N2 - 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. SN - 1476-4687 UR - https://www.unboundmedicine.com/medline/citation/29143815/Genome_sequence_of_the_progenitor_of_the_wheat_D_genome_Aegilops_tauschii_ L2 - https://doi.org/10.1038/nature24486 DB - PRIME DP - Unbound Medicine ER -