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

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

doi:10.1186/s13059-015-0582-8

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

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

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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.

Original language	English
Article number	26
Pages (from-to)	1-17
Number of pages	17
Journal	Genome Biology
Volume	16
Issue number	1
DOIs	https://doi.org/10.1186/s13059-015-0582-8
Publication status	Published - 31 Jan 2015

ASJC Scopus subject areas

Ecology, Evolution, Behavior and Systematics
Genetics
Cell Biology

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Final published version
© 2015 Chapman et al.; licensee BioMed Central. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
Final published version, 1.77 MBLicence: CC BY

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Chapman, J. A., Mascher, M., Buluç, A., Barry, K., Georganas, E., Session, A., Strnadova, V., Jenkins, J., Sehgal, S., Oliker, L., Schmutz, J., Yelick, K. A., Scholz, U., Waugh, R., Poland, J. A., Muehlbauer, G. J., Stein, N., & Rokhsar, D. S. (2015). A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome. Genome Biology, 16(1), 1-17. Article 26. https://doi.org/10.1186/s13059-015-0582-8

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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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Chapman, JA, Mascher, M, Buluç, A, Barry, K, Georganas, E, Session, A, Strnadova, V, Jenkins, J, Sehgal, S, Oliker, L, Schmutz, J, Yelick, KA, Scholz, U, Waugh, R, Poland, JA, Muehlbauer, GJ, Stein, N & Rokhsar, DS 2015, 'A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome', Genome Biology, vol. 16, no. 1, 26, pp. 1-17. https://doi.org/10.1186/s13059-015-0582-8

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AU - Session, Adam

AU - Strnadova, Veronika

AU - Jenkins, Jerry

AU - Sehgal, Sunish

AU - Oliker, Leonid

AU - Schmutz, Jeremy

AU - Yelick, Katherine A.

AU - Scholz, Uwe

AU - Waugh, Robbie

AU - Poland, Jesse A.

AU - Muehlbauer, Gary J.

AU - Stein, Nils

AU - Rokhsar, Daniel S.

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

Abstract

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