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

Jarrod A Chapman; Martin Mascher; Aydın 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

Genome Biol. 2015 Jan 31;16(1):26. doi: 10.1186/s13059-015-0582-8.

Authors

Jarrod A Chapman¹, Martin Mascher², Aydın Buluç³, Kerrie Barry⁴, Evangelos Georganas^{5

6}, Adam Session⁷, Veronika Strnadova⁸, Jerry Jenkins^{9

10}, Sunish Sehgal^{11

12}, Leonid Oliker¹³, Jeremy Schmutz^{14

15}, Katherine A Yelick^{16

17}, Uwe Scholz¹⁸, Robbie Waugh¹⁹, Jesse A Poland²⁰, Gary J Muehlbauer²¹, Nils Stein²², Daniel S Rokhsar^{23

24}

Affiliations

¹ Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA. jarrodc@gmail.com.
² Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Stadt Seeland, Germany. mascher@ipk-gatersleben.de.
³ Computational Research Division and National Energy Research Supercomputing Center (NERSC), Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. abuluc@lbl.gov.
⁴ Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA. kwbarry@lbl.gov.
⁵ Computational Research Division and National Energy Research Supercomputing Center (NERSC), Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. egeor@eecs.berkeley.edu.
⁶ Department of Electrical Engineering and Computer Science, Computer Science Division, University of California, Berkeley, CA, 94720, USA. egeor@eecs.berkeley.edu.
⁷ Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA. adamsession@berkeley.edu.
⁸ Department of Computer Science, University of California, Santa Barbara, CA, 93106, USA. veronika@cs.ucsb.edu.
⁹ Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA. jjenkins@hudsonalpha.org.
¹⁰ HudsonAlpha Institute of Biotechnology, Huntsville, AL, 35806, USA. jjenkins@hudsonalpha.org.
¹¹ Department of Plant Pathology, Kansas State University, Manhattan, KS, 65506, USA. sunish.sehgal@sdstate.edu.
¹² Present address: Department of Plant Science, South Dakota State University, Brookings, SD, 57007, USA. sunish.sehgal@sdstate.edu.
¹³ Computational Research Division and National Energy Research Supercomputing Center (NERSC), Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. loliker@lbl.gov.
¹⁴ Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA. jschmutz@hudsonalpha.org.
¹⁵ HudsonAlpha Institute of Biotechnology, Huntsville, AL, 35806, USA. jschmutz@hudsonalpha.org.
¹⁶ Computational Research Division and National Energy Research Supercomputing Center (NERSC), Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. yelick@eecs.berkeley.edu.
¹⁷ Department of Electrical Engineering and Computer Science, Computer Science Division, University of California, Berkeley, CA, 94720, USA. yelick@eecs.berkeley.edu.
¹⁸ Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Stadt Seeland, Germany. scholz@ipk-gatersleben.de.
¹⁹ Division of Plant Sciences, University of Dundee & The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK. Robbie.Waugh@hutton.ac.uk.
²⁰ Department of Plant Pathology, Kansas State University, Manhattan, KS, 65506, USA. jpoland@ksu.edu.
²¹ Departments of Agronomy and Plant Genetics, and Plant Biology, University of Minnesota, St Paul, MN, 55108, USA. muehl003@umn.edu.
²² Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Stadt Seeland, Germany. stein@ipk-gatersleben.de.
²³ Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA. dsrokhsar@gmail.com.
²⁴ Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA. dsrokhsar@gmail.com.

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.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Bread*
Chromosome Mapping
Contig Mapping
DNA, Complementary / genetics
Genetic Linkage
Genetic Variation
Genome, Plant*
Homozygote
Nucleotides / genetics
Polyploidy*
Reproducibility of Results
Sequence Analysis, DNA / methods*
Triticum / genetics*

Substances

DNA, Complementary
Nucleotides

Grants and funding

BB/I00663X/1/Biotechnology and Biological Sciences Research Council/United Kingdom