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

Agronomy and Plant Genetics

Research output: Contribution to journal › Article › peer-review

199 Scopus citations

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 (US)
Article number	26
Journal	Genome biology
Volume	16
Issue number	1
DOIs	https://doi.org/10.1186/s13059-015-0582-8
State	Published - Jan 31 2015

Bibliographical note

Funding Information:
The work performed by the US Department of Energy Joint Genome Institute is supported by the Office of Science of the US Department of Energy under contract number DE-AC02-05CH11231. The authors would also like to acknowledge the support given by funds received from the Triticeae Coordinated Agricultural Project, US Department of Agriculture/ National Institute for Food and Agriculture grant number 2011-68002-30029 to GJM and JAP, the Kansas Wheat Commission, Kansas Wheat Alliance, The Bill and Melinda Gates Foundation, US National Science Foundation, and USAID to JAP, the Scottish Government Rural and Environment Science and Analytical Services Division and BBSRC grant number BB/I00663X/1 to RW, and the Bundesministerium fur Bildung und Forschung Plant2030 program (TRITEX 0315954, NUGGET 0315957A) to NS and US Research at the Computational Research Division/Lawrence Berkeley National Laboratory is supported in part by the Department of Energy, Office of Science, contract number DE-AC02-05CH11231. This work used resources of the National Energy Research Scientific Computing Center, which is supported by the Office of Science of the US Department of Energy under contract DE-AC02-05CH11231. EG acknowledges the support of the US DOE grant DE-SC0008700. AS acknowledges support from the NHGRI Berkeley Training Grant in Genomics. We thank Lisa Borello for helpful comments on the manuscript. We are grateful to Doreen Stengel, Daniel Arend and Matthias Lange for help with data submission. We thank the International Wheat Genome Sequencing Consortium for making their chromosome-by-chromosome shotgun assemblies available prior to publication.

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© 2015 Chapman et al. licensee BioMed Central.

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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), Article 26. https://doi.org/10.1186/s13059-015-0582-8

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. 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.",

author = "Chapman, {Jarrod A.} and Martin Mascher and Aydin Bulu{\c c} and Kerrie Barry and Evangelos Georganas and Adam Session and Veronika Strnadova and Jerry Jenkins and Sunish Sehgal and Leonid Oliker and Jeremy Schmutz and Yelick, {Katherine A.} and Uwe Scholz and Robbie Waugh and Poland, {Jesse A.} and Muehlbauer, {Gary J.} and Nils Stein and Rokhsar, {Daniel S.}",

note = "Funding Information: The work performed by the US Department of Energy Joint Genome Institute is supported by the Office of Science of the US Department of Energy under contract number DE-AC02-05CH11231. The authors would also like to acknowledge the support given by funds received from the Triticeae Coordinated Agricultural Project, US Department of Agriculture/ National Institute for Food and Agriculture grant number 2011-68002-30029 to GJM and JAP, the Kansas Wheat Commission, Kansas Wheat Alliance, The Bill and Melinda Gates Foundation, US National Science Foundation, and USAID to JAP, the Scottish Government Rural and Environment Science and Analytical Services Division and BBSRC grant number BB/I00663X/1 to RW, and the Bundesministerium fur Bildung und Forschung Plant2030 program (TRITEX 0315954, NUGGET 0315957A) to NS and US Research at the Computational Research Division/Lawrence Berkeley National Laboratory is supported in part by the Department of Energy, Office of Science, contract number DE-AC02-05CH11231. This work used resources of the National Energy Research Scientific Computing Center, which is supported by the Office of Science of the US Department of Energy under contract DE-AC02-05CH11231. EG acknowledges the support of the US DOE grant DE-SC0008700. AS acknowledges support from the NHGRI Berkeley Training Grant in Genomics. We thank Lisa Borello for helpful comments on the manuscript. We are grateful to Doreen Stengel, Daniel Arend and Matthias Lange for help with data submission. We thank the International Wheat Genome Sequencing Consortium for making their chromosome-by-chromosome shotgun assemblies available prior to publication. Publisher Copyright: {\textcopyright} 2015 Chapman et al. licensee BioMed Central.",

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AU - Chapman, Jarrod A.

AU - Mascher, Martin

AU - Buluç, Aydin

AU - Barry, Kerrie

AU - Georganas, Evangelos

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

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