A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome

被引：192

作者：

Chapman, Jarrod A. ^{[1
]}

Mascher, Martin ^{[2
,3
]}

Buluc, Aydin ^{[4
,5
]}

Barry, Kerrie ^{[1
,4
]}

Georganas, Evangelos ^{[4
,5
,6
]}

Session, Adam ^{[7
]}

Strnadova, Veronika ^{[8
]}

Jenkins, Jerry ^{[1
]}

Sehgal, Sunish ^{[10
]}

Oliker, Leonid ^{[4
,5
]}

Schmutz, Jeremy ^{[1
,9
]}

Yelick, Katherine A. ^{[4
,5
,6
]}

Scholz, Uwe ^{[2
,3
]}

Waugh, Robbie ^{[11
]}

Poland, Jesse A.

Muehlbauer, Gary J. ^{[12
,13
]}

Stein, Nils ^{[2
,3
]}

Rokhsar, Daniel S. ^{[1
,7
]}

机构：

[1] Joint Genome Inst, Dept Energy, Walnut Creek, CA 94598 USA

[2] Leibniz Inst Plant Genet, D-06466 Stadt Seeland, Germany

[3] Crop Plant Res IPK Gatersleben, D-06466 Stadt Seeland, Germany

[4] Computat Res Div, Berkeley, CA 94720 USA

[5] NERSC, Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA

[6] Univ Calif Berkeley, Div Comp Sci, Dept Elect Engn & Comp Sci, Berkeley, CA 94720 USA

[7] Univ Calif Berkeley, Dept Mol & Cell Biol, Berkeley, CA 94720 USA

[8] Univ Calif Santa Barbara, Dept Comp Sci, Santa Barbara, CA 93106 USA

[9] HudsonAlpha Inst Biotechnol, Huntsville, AL 35806 USA

[10] Kansas State Univ, Dept Plant Pathol, Manhattan, KS 66506 USA

[11] Univ Dundee & James Hutton Inst, Div Plant Sci, Dundee DD2 5DA, Scotland

[12] Univ Minnesota, Dept Agron & Plant Genet, St Paul, MN 55108 USA

[13] Univ Minnesota, Dept Plant Biol, St Paul, MN 55108 USA

来源：

GENOME BIOLOGY | 2015年 / 16卷

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：

COPY NUMBER VARIATION; AEGILOPS-TAUSCHII; PHYSICAL MAP; DRAFT GENOME; HIGH-DENSITY; SEQUENCE; DIVERSITY; DATABASE; REVEALS; CAPTURE;

D O I：

10.1186/s13059-015-0582-8

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

Polyploid species have long been thought to be recalcitrant to whole-genome assembly. By combining high-throughput sequencing, recent developments in parallel computing, and genetic mapping, we derive, de novo, a sequence assembly representing 9.1 Gbp of the highly repetitive 16 Gbp genome of hexaploid wheat, Triticum aestivum, and assign 7.1 Gb of this assembly to chromosomal locations. The genome representation and accuracy of our assembly is comparable or even exceeds that of a chromosome-by-chromosome shotgun assembly. Our assembly and mapping strategy uses only short read sequencing technology and is applicable to any species where it is possible to construct a mapping population.

引用

页数：17

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