Genome sequence of the progenitor of the wheat D genome Aegilops tauschii

被引：467

作者：

Luo, Ming-Cheng ^{[1
]}

Gu, Yong Q. ^{[2
]}

Puiu, Daniela ^{[3
]}

Wang, Hao ^{[4
,5
,6
]}

Twardziok, Sven O. ^{[7
]}

Deal, Karin R. ^{[1
]}

Huo, Naxin ^{[1
,2
]}

Zhu, Tingting ^{[1
]}

Wang, Le ^{[1
]}

Wang, Yi ^{[1
,2
]}

McGuire, Patrick E. ^{[1
]}

Liu, Shuyang ^{[1
]}

Long, Hai ^{[1
]}

Ramasamy, Ramesh K. ^{[1
]}

Rodriguez, Juan C. ^{[1
]}

Van, Sonny L. ^{[1
]}

Yuan, Luxia ^{[1
]}

Wang, Zhenzhong ^{[1
,8
]}

Xia, Zhiqiang ^{[1
]}

Xiao, Lichan ^{[1
]}

Anderson, Olin D. ^{[2
]}

Ouyang, Shuhong ^{[2
,8
]}

Liang, Yong ^{[2
,8
]}

Zimin, Aleksey V. ^{[3
]}

Pertea, Geo ^{[3
]}

Qi, Peng ^{[4
,5
]}

Ennetzen, Jeffrey L. B. ^{[6
]}

Dai, Xiongtao ^{[9
]}

Dawson, Matthew W. ^{[9
]}

Mueller, Hans-Georg ^{[9
]}

Kugler, Karl ^{[7
]}

Rivarola-Duarte, Lorena ^{[7
]}

Spannagl, Manuel ^{[7
]}

Mayer, Klaus F. X. ^{[7
,10
]}

Lu, Fu-Hao ^{[11
]}

Bevan, Michael W. ^{[11
]}

Leroy, Philippe ^{[12
]}

Li, Pingchuan ^{[13
]}

You, Frank M. ^{[13
]}

Sun, Qixin ^{[8
]}

Liu, Zhiyong ^{[8
]}

Lyons, Eric ^{[14
]}

Wicker, Thomas ^{[15
]}

Salzberg, Steven L. ^{[3
,16
,17
,18
]}

Devos, Katrien M. ^{[4
,5
]}

Dvorak, Jan ^{[1
]}

机构：

[1] Univ Calif Davis, Dept Plant Sci, Davis, CA 95616 USA

[2] USDA ARS, Crop Improvement & Genet Res, Albany, CA USA

[3] Johns Hopkins Univ, Sch Med, McKusick Nathans Inst Genet Med, Ctr Computat Biol, Baltimore, MD 21218 USA

[4] Univ Georgia, Dept Crop & Soil Sci, Inst Plant Breeding Genet & Genom, Athens, GA 30602 USA

[5] Univ Georgia, Dept Plant Sci, Athens, GA 30602 USA

[6] Univ Georgia, Dept Genet, Athens, GA 30602 USA

[7] Helmholtz Zentrum M nchen, Plant Genome & Syst Biol, Neuherberg, Germany

[8] China Agr Univ, Beijing, Peoples R China

[9] Univ Calif Davis, Dept Stat, Davis, CA 95616 USA

[10] Tech Univ Munich, Sch Life Sci Weihenstephan, Munich, Germany

[11] Norwich Res Pk, John Innes Ctr, Dept Cell & Dev Biol, Norwich, Norfolk, England

[12] INRA, UBP, UMR 1095, GDEC, Clermont Ferrand, France

[13] Agr & Agri Food Canada, Morden, MB, Canada

[14] Univ Arizona, CyVerse, Tucson, AZ USA

[15] Univ Zurich, Dept Plant & Microbial Biol, Zurich, Switzerland

[16] Johns Hopkins Univ, Dept Biomed Engn, Baltimore, MD 21218 USA

[17] Johns Hopkins Univ, Dept Comp Sci, Baltimore, MD 21218 USA

[18] Johns Hopkins Univ, Dept Biostat, Baltimore, MD 21205 USA

来源：

NATURE | 2017年 / 551卷 / 7681期

基金：

英国生物技术与生命科学研究理事会; 美国国家科学基金会;

关键词：

POLYPLOID WHEAT; ORYZA-SATIVA; GENE; EVOLUTION; RECOMBINATION; RESISTANCE; FAMILIES; IDENTIFICATION; ANNOTATION; DIVERGENCE;

D O I：

10.1038/nature24486

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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(2-4). 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.

引用

页码：498 / +

页数：22

共 75 条

[1] BASIC LOCAL ALIGNMENT SEARCH TOOL [J].

ALTSCHUL, SF ;

GISH, W ;

MILLER, W ;

MYERS, EW ;

LIPMAN, DJ .

JOURNAL OF MOLECULAR BIOLOGY, 1990, 215 (03) :403-410

[2] Analysis of the genome sequence of the flowering plant Arabidopsis thaliana [J].

Kaul, S ;

Koo, HL ;

Jenkins, J ;

Rizzo, M ;

Rooney, T ;

Tallon, LJ ;

Feldblyum, T ;

Nierman, W ;

Benito, MI ;

Lin, XY ;

Town, CD ;

Venter, JC ;

Fraser, CM ;

Tabata, S ;

Nakamura, Y ;

Kaneko, T ;

Sato, S ;

Asamizu, E ;

Kato, T ;

Kotani, H ;

Sasamoto, S ;

Ecker, JR ;

Theologis, A ;

Federspiel, NA ;

Palm, CJ ;

Osborne, BI ;

Shinn, P ;

Conway, AB ;

Vysotskaia, VS ;

Dewar, K ;

Conn, L ;

Lenz, CA ;

Kim, CJ ;

Hansen, NF ;

Liu, SX ;

Buehler, E ;

Altafi, H ;

Sakano, H ;

Dunn, P ;

Lam, B ;

Pham, PK ;

Chao, Q ;

Nguyen, M ;

Yu, GX ;

Chen, HM ;

Southwick, A ;

Lee, JM ;

Miranda, M ;

Toriumi, MJ ;

Davis, RW .

NATURE, 2000, 408 (6814) :796-815

[3]

Arumuganathan K., 1991, Plant Mol Biol Rep, V9, P208, DOI [10.1007/BF02672069, DOI 10.1007/BF02672069]

[4] Exceptional Diversity, Non-Random Distribution, and Rapid Evolution of Retroelements in the B73 Maize Genome [J].

Baucom, Regina S. ;

Estill, James C. ;

Chaparro, Cristian ;

Upshaw, Naadira ;

Jogi, Ansuya ;

Deragon, Jean-Marc ;

Westerman, Richard P. ;

SanMiguel, Phillip J. ;

Bennetzen, Jeffrey L. .

PLOS GENETICS, 2009, 5 (11)

[5] Comparative physical mapping links conservation of microsynteny to chromosome structure and recombination in grasses [J].

Bowers, JE ;

Arias, MA ;

Asher, R ;

Avise, JA ;

Ball, RT ;

Brewer, GA ;

Buss, RW ;

Chen, AH ;

Edwards, TM ;

Estill, JC ;

Exum, HE ;

Goff, VH ;

Herrick, KL ;

Steele, CLJ ;

Karunakaran, S ;

Lafayette, GK ;

Lemke, C ;

Marler, BS ;

Masters, SL ;

McMillan, JM ;

Nelson, LK ;

Newsome, GA ;

Nwakanma, CC ;

Odeh, RN ;

Phelps, CA ;

Rarick, EA ;

Rogers, CJ ;

Ryan, SP ;

Slaughter, KA ;

Soderlund, CA ;

Tang, HB ;

Wing, RA ;

Paterson, AH .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2005, 102 (37) :13206-13211

[6] Rapid detection of structural variation in a human genome using nanochannel-based genome mapping technology [J].

Cao, Hongzhi ;

Hastie, Alex R. ;

Cao, Dandan ;

Lam, Ernest T. ;

Sun, Yuhui ;

Huang, Haodong ;

Liu, Xiao ;

Lin, Liya ;

Andrews, Warren ;

Chan, Saki ;

Huang, Shujia ;

Tong, Xin ;

Requa, Michael ;

Anantharaman, Thomas ;

Krogh, Anders ;

Yang, Huanming ;

Cao, Han ;

Xu, Xun .

GIGASCIENCE, 2014, 3

[7] Molecular basis of evolutionary events that shaped the hardness locus in diploid and polyploid wheat species (Triticum and aegilops) [J].

Chantret, N ;

Salse, J ;

Sabot, F ;

Rahman, S ;

Bellec, A ;

Laubin, B ;

Dubois, I ;

Dossat, C ;

Sourdille, P ;

Joudrier, P ;

Gautier, MF ;

Cattolico, L ;

Beckert, M ;

Aubourg, S ;

Weissenbach, J ;

Caboche, M ;

Bernard, M ;

Leroy, P ;

Chalhoub, B .

PLANT CELL, 2005, 17 (04) :1033-1045

[8] An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations [J].

Clavijo, Bernardo J. ;

Venturini, Luca ;

Schudoma, Christian ;

Accinelli, Gonzalo Garcia ;

Kaithakottil, Gemy ;

Wright, Jonathan ;

Borrill, Philippa ;

Kettleborough, George ;

Heavens, Darren ;

Chapman, Helen ;

Lipscombe, James ;

Barker, Tom ;

Lu, Fu-Hao ;

McKenzie, Neil ;

Raats, Dina ;

Ramirez-Gonzalez, Ricardo H. ;

Coince, Aurore ;

Peel, Ned ;

Percival-Alwyn, Lawrence ;

Duncan, Owen ;

Troesch, Josua ;

Yu, Guotai ;

Bolser, Dan M. ;

Namaati, Guy ;

Kerhornou, Arnaud ;

Spannagl, Manuel ;

Gundlach, Heidrun ;

Haberer, Georg ;

Davey, Robert P. ;

Fosker, Christine ;

Di Palma, Federica ;

Phillips, Andrew L. ;

Millar, A. Harvey ;

Kersey, Paul J. ;

Uauy, Cristobal ;

Krasileva, Ksenia V. ;

Swarbreck, David ;

Bevan, Michael W. ;

Clark, Matthew D. .

GENOME RESEARCH, 2017, 27 (05) :885-896

[9] STRUCTURAL EVOLUTION OF WHEAT CHROMOSOMES 4A, 5A, AND 7B AND ITS IMPACT ON RECOMBINATION [J].

DEVOS, KM ;

DUBCOVSKY, J ;

DVORAK, J ;

CHINOY, CN ;

GALE, MD .

THEORETICAL AND APPLIED GENETICS, 1995, 91 (02) :282-288

[10] Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis [J].

Devos, KM ;

Brown, JKM ;

Bennetzen, JL .

GENOME RESEARCH, 2002, 12 (07) :1075-1079

← 1 2 3 4 5 6 7 8 →