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

Jarrod Chapman(Joint Genome Institute), Martin Mascher(Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)), Aydın Buluç(Lawrence Berkeley National Laboratory), Kerrie Barry(Joint Genome Institute), Evangelos Georganas(Lawrence Berkeley National Laboratory), Adam M. Session(University of California, Berkeley), Veronika Strnadova(University of California, Santa Barbara), Jerry Jenkins(Joint Genome Institute), Sunish K. Sehgal(South Dakota State University), Leonid Oliker(Lawrence Berkeley National Laboratory), Jeremy Schmutz(Joint Genome Institute), Katherine Yelick(Lawrence Berkeley National Laboratory), Uwe Scholz(Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)), Robbie Waugh(James Hutton Institute), Jesse Poland(Kansas State University), Gary J. Muehlbauer(University of Minnesota), Nils Stein(Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)), Daniel S. Rokhsar(Joint Genome Institute)
Genome Biology
January 30, 2015
10.1186/s13059-015-0582-8
Cited by 259Open Access
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Abstract

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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