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author Luo, Ming-Cheng
Gu, Yong Q.
Puiu, Daniela
Wang, Hao
Twardziok, Sven O.
Deal, Karin R.
Huo, Naxin
Zhu, Tingting
Wang, Le
Wang, Yi
McGuire, Patrick E.
Liu, Shuyang
Long, Hai
Ramasamy, Ramesh K.
Rodriguez, Juan C.
Van, Sonny L.
Yuan, Luxia
Wang, Zhenzhong
Xia, Zhiqiang
Xiao, Lichan
Anderson, Olin D.
Ouyang, Shuhong
Liang, Yong
Zimin, Aleksey V.
Pertea, Geo
Qi, Peng
Bennetzen, Jeffrey L.
Dai, Xiongtao
Dawson, Matthew W.
Müller, Hans-Georg
Kugler, Karl
Rivarola-Duarte, Lorena
Spannagl, Manuel
Mayer, Klaus F. X.
Lu, Fu-Hao
Bevan, Michael W.
Leroy, Philippe
Li, Pingchuan
You, Frank M.
Sun, Qixin
Liu, Zhiyong
Lyons, Eric
Wicker, Thomas
Salzberg, Steven L.
Devos, Katrien M.
Dvořák, Jan
author_facet Luo, Ming-Cheng
Gu, Yong Q.
Puiu, Daniela
Wang, Hao
Twardziok, Sven O.
Deal, Karin R.
Huo, Naxin
Zhu, Tingting
Wang, Le
Wang, Yi
McGuire, Patrick E.
Liu, Shuyang
Long, Hai
Ramasamy, Ramesh K.
Rodriguez, Juan C.
Van, Sonny L.
Yuan, Luxia
Wang, Zhenzhong
Xia, Zhiqiang
Xiao, Lichan
Anderson, Olin D.
Ouyang, Shuhong
Liang, Yong
Zimin, Aleksey V.
Pertea, Geo
Qi, Peng
Bennetzen, Jeffrey L.
Dai, Xiongtao
Dawson, Matthew W.
Müller, Hans-Georg
Kugler, Karl
Rivarola-Duarte, Lorena
Spannagl, Manuel
Mayer, Klaus F. X.
Lu, Fu-Hao
Bevan, Michael W.
Leroy, Philippe
Li, Pingchuan
You, Frank M.
Sun, Qixin
Liu, Zhiyong
Lyons, Eric
Wicker, Thomas
Salzberg, Steven L.
Devos, Katrien M.
Dvořák, Jan
author_sort Luo, Ming-Cheng
collection PubMed
description Aegilops tauschii is the diploid progenitor of the D genome of hexaploid wheat(1) (Triticum aestivum, genomes AABBDD) and an important genetic resource for wheat(2,3,4). The large size and highly repetitive nature of the Ae. tauschii genome has until now precluded the development of a reference-quality genome sequence(5). 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. SUPPLEMENTARY INFORMATION: The online version of this article (doi:10.1038/nature24486) contains supplementary material, which is available to authorized users.
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spelling pubmed-74166252020-08-17 Genome sequence of the progenitor of the wheat D genome Aegilops tauschii Luo, Ming-Cheng Gu, Yong Q. Puiu, Daniela Wang, Hao Twardziok, Sven O. Deal, Karin R. Huo, Naxin Zhu, Tingting Wang, Le Wang, Yi McGuire, Patrick E. Liu, Shuyang Long, Hai Ramasamy, Ramesh K. Rodriguez, Juan C. Van, Sonny L. Yuan, Luxia Wang, Zhenzhong Xia, Zhiqiang Xiao, Lichan Anderson, Olin D. Ouyang, Shuhong Liang, Yong Zimin, Aleksey V. Pertea, Geo Qi, Peng Bennetzen, Jeffrey L. Dai, Xiongtao Dawson, Matthew W. Müller, Hans-Georg Kugler, Karl Rivarola-Duarte, Lorena Spannagl, Manuel Mayer, Klaus F. X. Lu, Fu-Hao Bevan, Michael W. Leroy, Philippe Li, Pingchuan You, Frank M. Sun, Qixin Liu, Zhiyong Lyons, Eric Wicker, Thomas Salzberg, Steven L. Devos, Katrien M. Dvořák, Jan Nature Article Aegilops tauschii is the diploid progenitor of the D genome of hexaploid wheat(1) (Triticum aestivum, genomes AABBDD) and an important genetic resource for wheat(2,3,4). The large size and highly repetitive nature of the Ae. tauschii genome has until now precluded the development of a reference-quality genome sequence(5). 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. SUPPLEMENTARY INFORMATION: The online version of this article (doi:10.1038/nature24486) contains supplementary material, which is available to authorized users. Nature Publishing Group UK 2017-11-01 2017 /pmc/articles/PMC7416625/ /pubmed/29143815 http://dx.doi.org/10.1038/nature24486 Text en © The Author(s) 2017 This work is licensed under a Creative Commons Attribution 4.0 International (CC BY 4.0) licence. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons licence, users will need to obtain permission from the licence holder to reproduce the material. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Luo, Ming-Cheng
Gu, Yong Q.
Puiu, Daniela
Wang, Hao
Twardziok, Sven O.
Deal, Karin R.
Huo, Naxin
Zhu, Tingting
Wang, Le
Wang, Yi
McGuire, Patrick E.
Liu, Shuyang
Long, Hai
Ramasamy, Ramesh K.
Rodriguez, Juan C.
Van, Sonny L.
Yuan, Luxia
Wang, Zhenzhong
Xia, Zhiqiang
Xiao, Lichan
Anderson, Olin D.
Ouyang, Shuhong
Liang, Yong
Zimin, Aleksey V.
Pertea, Geo
Qi, Peng
Bennetzen, Jeffrey L.
Dai, Xiongtao
Dawson, Matthew W.
Müller, Hans-Georg
Kugler, Karl
Rivarola-Duarte, Lorena
Spannagl, Manuel
Mayer, Klaus F. X.
Lu, Fu-Hao
Bevan, Michael W.
Leroy, Philippe
Li, Pingchuan
You, Frank M.
Sun, Qixin
Liu, Zhiyong
Lyons, Eric
Wicker, Thomas
Salzberg, Steven L.
Devos, Katrien M.
Dvořák, Jan
Genome sequence of the progenitor of the wheat D genome Aegilops tauschii
title Genome sequence of the progenitor of the wheat D genome Aegilops tauschii
title_full Genome sequence of the progenitor of the wheat D genome Aegilops tauschii
title_fullStr Genome sequence of the progenitor of the wheat D genome Aegilops tauschii
title_full_unstemmed Genome sequence of the progenitor of the wheat D genome Aegilops tauschii
title_short Genome sequence of the progenitor of the wheat D genome Aegilops tauschii
title_sort genome sequence of the progenitor of the wheat d genome aegilops tauschii
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7416625/
https://www.ncbi.nlm.nih.gov/pubmed/29143815
http://dx.doi.org/10.1038/nature24486
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