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

Chapman, Jarrod A.; Mascher, Martin; Buluc, Aydin; Barry, Kerrie; Georganas, Evangelos; Session, Adam; Strnadova, Veronika; Jenkins, Jerry; Sehgal, Sunish; Oliker, Leonid; Schmutz, Jeremy; Yelick, Katherine A.; Scholz, Uwe; Waugh, Robbie; Poland, Jesse A.; Muehlbauer, Gary J.; Stein, Nils; Rokhsar, Daniel S.

doi:10.1186/s13059-015-0582-8

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

Journal Article · Sat Jan 31 00:00:00 EST 2015 · GenomeBiology.com

DOI:https://doi.org/10.1186/s13059-015-0582-8· OSTI ID:1256489

Chapman, Jarrod A. ^[1]; Mascher, Martin ^[2]; Buluc, Aydin ^[3]; Barry, Kerrie ^[1]; Georganas, Evangelos ^[4]; Session, Adam ^[5]; Strnadova, Veronika ^[5]; Jenkins, Jerry ^[6]; Sehgal, Sunish ^[7]; Oliker, Leonid ^[3]; Schmutz, Jeremy ^[6]; Yelick, Katherine A. ^[4]; Scholz, Uwe ^[2]; Waugh, Robbie ^[8]; Poland, Jesse A. ^[9]; Muehlbauer, Gary J. ^[10]; Stein, Nils ^[2]; Rokhsar, Daniel S. ^[11]

Department of Energy Joint Genome Institute, Walnut Creek, CA (United States)
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben (Germany)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States)
Univ. of California, Berkeley, CA (United States)
Department of Energy Joint Genome Institute, Walnut Creek, CA (United States); HudsonAlpha Institute of Biotechnology, Huntsville, AL (United States)
Kansas State Univ., Manhattan, KS (United States); South Dakota State Univ., Brookings, SD (United States)
Univ. of Dundee & The James Hutton Institute, Dundee (United Kingdom)
Kansas State Univ., Manhattan, KS (United States)
Univ. of Minnesota, St. Paul, MN (United States)
Department of Energy Joint Genome Institute, Walnut Creek, CA (United States); Univ. of California, Berkeley, CA (United States)

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.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: AC02-05CH11231; SC0008700

OSTI ID:: 1256489

Alternate ID(s):: OSTI ID: 1524013

Journal Information:: GenomeBiology.com, Vol. 16, Issue 1; ISSN 1465-6906

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 184 works

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