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

被引：287

作者：

Clavijo, Bernardo J. ^{[1
]}

Venturini, Luca ^{[1
]}

Schudoma, Christian ^{[1
]}

Accinelli, Gonzalo Garcia ^{[1
]}

Kaithakottil, Gemy ^{[1
]}

Wright, Jonathan ^{[1
]}

Borrill, Philippa ^{[2
]}

Kettleborough, George ^{[1
]}

Heavens, Darren ^{[1
]}

Chapman, Helen ^{[1
]}

Lipscombe, James ^{[1
]}

Barker, Tom ^{[1
]}

Lu, Fu-Hao ^{[2
]}

McKenzie, Neil ^{[2
]}

Raats, Dina ^{[1
]}

Ramirez-Gonzalez, Ricardo H. ^{[1
,2
]}

Coince, Aurore ^{[1
]}

Peel, Ned ^{[1
]}

Percival-Alwyn, Lawrence ^{[1
]}

Duncan, Owen ^{[3
]}

Troesch, Josua ^{[3
]}

Yu, Guotai ^{[2
]}

Bolser, Dan M. ^{[4
]}

Namaati, Guy ^{[4
]}

Kerhornou, Arnaud ^{[4
]}

Spannagl, Manuel ^{[5
]}

Gundlach, Heidrun ^{[5
]}

Haberer, Georg ^{[5
]}

Davey, Robert P. ^{[1
,6
]}

Fosker, Christine ^{[1
]}

Di Palma, Federica ^{[1
,6
]}

Phillips, Andrew L. ^{[7
]}

Millar, A. Harvey ^{[3
]}

Kersey, Paul J. ^{[4
]}

Uauy, Cristobal ^{[2
]}

Krasileva, Ksenia V. ^{[1
,6
,8
]}

Swarbreck, David ^{[1
,6
]}

Bevan, Michael W. ^{[2
]}

Clark, Matthew D. ^{[1
,6
]}

机构：

[1] Earlham Inst, Norwich NR4 7UZ, Norfolk, England

[2] John Innes Ctr, Norwich NR4 7UH, Norfolk, England

[3] Univ Western Australia, ARC Ctr Excellence Plant Energy Biol, Crawley, WA 6009, Australia

[4] EMBL European Bioinformat Inst, Hinxton CB10 1SD, England

[5] Helmholtz Ctr Munich, Plant Genome & Syst Biol, D-85764 Neuherberg, Germany

[6] Univ East Anglia, Norwich NR4 7TJ, Norfolk, England

[7] Rothamsted Res, Harpenden AL5 2JQ, Herts, England

[8] Sainsbury Lab, Norwich NR4 7UH, Norfolk, England

来源：

GENOME RESEARCH | 2017年 / 27卷 / 05期

基金：

澳大利亚研究理事会; 英国生物技术与生命科学研究理事会;

关键词：

TRANSCRIPTOME; REVEALS; RECONSTRUCTION; GENERATION; EXPRESSION; EVOLUTION; INSIGHTS; GRASSES;

D O I：

10.1101/gr.217117.116

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Advances in genome sequencing and assembly technologies are generating many high-quality genome sequences, but assemblies of large, repeat-rich polyploid genomes, such as that of bread wheat, remain fragmented and incomplete. We have generated a new wheat whole-genome shotgun sequence assembly using a combination of optimized data types and an assembly algorithm designed to deal with large and complex genomes. The new assembly represents >78% of the genome with a scaffold N50 of 88.8 kb that has a high fidelity to the input data. Our new annotation combines strand-specific Illumina RNA-seq and Pacific Biosciences (PacBio) full-length cDNAs to identify 104,091 high-confidence protein-coding genes and 10,156 noncoding RNA genes. We confirmed three known and identified one novel genome rearrangements. Our approach enables the rapid and scalable assembly of wheat genomes, the identification of structural variants, and the definition of complete gene models, all powerful resources for trait analysis and breeding of this key global crop.

引用

页码：885 / 896

页数：12

共 61 条

[1] A survey of the sorghum transcriptome using single-molecule long reads [J].

Abdel-Ghany, Salah E. ;

Hamilton, Michael ;

Jacobi, Jennifer L. ;

Ngam, Peter ;

Devitt, Nicholas ;

Schilkey, Faye ;

Ben-Hur, Asa ;

Reddy, Anireddy S. N. .

NATURE COMMUNICATIONS, 2016, 7

[2] Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries [J].

Aird, Daniel ;

Ross, Michael G. ;

Chen, Wei-Sheng ;

Danielsson, Maxwell ;

Fennell, Timothy ;

Russ, Carsten ;

Jaffe, David B. ;

Nusbaum, Chad ;

Gnirke, Andreas .

GENOME BIOLOGY, 2011, 12 (02)

[3] A map of human genome variation from population-scale sequencing [J].

Altshuler, David ;

Durbin, Richard M. ;

Abecasis, Goncalo R. ;

Bentley, David R. ;

Chakravarti, Aravinda ;

Clark, Andrew G. ;

Collins, Francis S. ;

De la Vega, Francisco M. ;

Donnelly, Peter ;

Egholm, Michael ;

Flicek, Paul ;

Gabriel, Stacey B. ;

Gibbs, Richard A. ;

Knoppers, Bartha M. ;

Lander, Eric S. ;

Lehrach, Hans ;

Mardis, Elaine R. ;

McVean, Gil A. ;

Nickerson, DebbieA. ;

Peltonen, Leena ;

Schafer, Alan J. ;

Sherry, Stephen T. ;

Wang, Jun ;

Wilson, Richard K. ;

Gibbs, Richard A. ;

Deiros, David ;

Metzker, Mike ;

Muzny, Donna ;

Reid, Jeff ;

Wheeler, David ;

Wang, Jun ;

Li, Jingxiang ;

Jian, Min ;

Li, Guoqing ;

Li, Ruiqiang ;

Liang, Huiqing ;

Tian, Geng ;

Wang, Bo ;

Wang, Jian ;

Wang, Wei ;

Yang, Huanming ;

Zhang, Xiuqing ;

Zheng, Huisong ;

Lander, Eric S. ;

Altshuler, David L. ;

Ambrogio, Lauren ;

Bloom, Toby ;

Cibulskis, Kristian ;

Fennell, Tim J. ;

Gabriel, Stacey B. .

NATURE, 2010, 467 (7319) :1061-1073

[4] The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates [J].

Berthelot, Camille ;

Brunet, Frederic ;

Chalopin, Domitille ;

Juanchich, Amelie ;

Bernard, Maria ;

Noel, Benjamin ;

Bento, Pascal ;

Da Silva, Corinne ;

Labadie, Karine ;

Alberti, Adriana ;

Aury, Jean-Marc ;

Louis, Alexandra ;

Dehais, Patrice ;

Bardou, Philippe ;

Montfort, Jerome ;

Klopp, Christophe ;

Cabau, Cedric ;

Gaspin, Christine ;

Thorgaard, Gary H. ;

Boussaha, Mekki ;

Quillet, Edwige ;

Guyomard, Rene ;

Galiana, Delphine ;

Bobe, Julien ;

Volff, Jean-Nicolas ;

Genet, Carine ;

Wincker, Patrick ;

Jaillon, Olivier ;

Roest Crollius, Hugues ;

Guiguen, Yann .

NATURE COMMUNICATIONS, 2014, 5

[5] Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome [J].

Bickhart, Derek M. ;

Rosen, Benjamin D. ;

Koren, Sergey ;

Sayre, Brian L. ;

Hastie, Alex R. ;

Chan, Saki ;

Lee, Joyce ;

Lam, Ernest T. ;

Liachko, Ivan ;

Sullivan, Shawn T. ;

Burton, Joshua N. ;

Huson, Heather J. ;

Nystrom, John C. ;

Kelley, Christy M. ;

Hutchison, Jana L. ;

Zhou, Yang ;

Sun, Jiajie ;

Crisa, Alessandra ;

de Leon, F. Abel Ponce ;

Schwartz, John C. ;

Hammond, John A. ;

Waldbieser, Geoffrey C. ;

Schroeder, Steven G. ;

Liu, George E. ;

Dunham, Maitreya J. ;

Shendure, Jay ;

Sonstegard, Tad S. ;

Phillippy, Adam M. ;

Van Tassell, Curtis P. ;

Smith, Timothy P. L. .

NATURE GENETICS, 2017, 49 (04) :643-+

[6] Read clouds uncover variation in complex regions of the human genome [J].

Bishara, Alex ;

Liu, Yuling ;

Weng, Ziming ;

Kashef-Haghighi, Dorna ;

Newburger, Daniel E. ;

West, Robert ;

Sidow, Arend ;

Batzoglou, Serafim .

GENOME RESEARCH, 2015, 25 (10) :1570-1580

[7] Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes [J].

Blanc, G ;

Wolfe, KH .

PLANT CELL, 2004, 16 (07) :1667-1678

[8] Genomics as the key to unlocking the polyploid potential of wheat [J].

Borrill, Philippa ;

Adamski, Nikolai ;

Uauy, Cristobal .

NEW PHYTOLOGIST, 2015, 208 (04) :1008-1022

[9] Analysis of the breadwheat genome using whole-genome shotgun sequencing [J].

Brenchley, Rachel ;

Spannagl, Manuel ;

Pfeifer, Matthias ;

Barker, Gary L. A. ;

D'Amore, Rosalinda ;

Allen, Alexandra M. ;

McKenzie, Neil ;

Kramer, Melissa ;

Kerhornou, Arnaud ;

Bolser, Dan ;

Kay, Suzanne ;

Waite, Darren ;

Trick, Martin ;

Bancroft, Ian ;

Gu, Yong ;

Huo, Naxin ;

Luo, Ming-Cheng ;

Sehgal, Sunish ;

Gill, Bikram ;

Kianian, Sharyar ;

Anderson, Olin ;

Kersey, Paul ;

Dvorak, Jan ;

McCombie, W. Richard ;

Hall, Anthony ;

Mayer, Klaus F. X. ;

Edwards, Keith J. ;

Bevan, Michael W. ;

Hall, Neil .

NATURE, 2012, 491 (7426) :705-710

[10] APPLICATIONS OF NEXT-GENERATION SEQUENCING Genetic variation and the de novo assembly of human genomes [J].

Chaisson, Mark J. P. ;

Wilson, Richard K. ;

Eichler, Evan E. .

NATURE REVIEWS GENETICS, 2015, 16 (11) :627-640

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