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PMID: 25637298 Published · epublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

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

Genome biology ·Vol. 16 ·2015-01-31 ·Pages 26

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

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.

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
Chemicals
DNA, Complementary Nucleotides
Authors & Affiliations
18 authors, click to expand affiliations / ORCID
Chapman Jarrod A
Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA. jarrodc@gmail.com.
Mascher Martin
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Stadt Seeland, Germany. mascher@ipk-gatersleben.de.
Buluç Aydın
Computational Research Division and National Energy Research Supercomputing Center (NERSC), Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. abuluc@lbl.gov.
Barry Kerrie
Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA. kwbarry@lbl.gov.
Georganas Evangelos
Computational Research Division and National Energy Research Supercomputing Center (NERSC), Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. egeor@eecs.berkeley.edu. | Department of Electrical Engineering and Computer Science, Computer Science Division, University of California, Berkeley, CA, 94720, USA. egeor@eecs.berkeley.edu.
Session Adam
Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA. adamsession@berkeley.edu.
Strnadova Veronika
Department of Computer Science, University of California, Santa Barbara, CA, 93106, USA. veronika@cs.ucsb.edu.
Jenkins Jerry
Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA. jjenkins@hudsonalpha.org. | HudsonAlpha Institute of Biotechnology, Huntsville, AL, 35806, USA. jjenkins@hudsonalpha.org.
Sehgal Sunish
Department of Plant Pathology, Kansas State University, Manhattan, KS, 65506, USA. sunish.sehgal@sdstate.edu. | Present address: Department of Plant Science, South Dakota State University, Brookings, SD, 57007, USA. sunish.sehgal@sdstate.edu.
Oliker Leonid
Computational Research Division and National Energy Research Supercomputing Center (NERSC), Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. loliker@lbl.gov.
Schmutz Jeremy
Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA. jschmutz@hudsonalpha.org. | HudsonAlpha Institute of Biotechnology, Huntsville, AL, 35806, USA. jschmutz@hudsonalpha.org.
Yelick Katherine A
Computational Research Division and National Energy Research Supercomputing Center (NERSC), Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. yelick@eecs.berkeley.edu. | Department of Electrical Engineering and Computer Science, Computer Science Division, University of California, Berkeley, CA, 94720, USA. yelick@eecs.berkeley.edu.
Scholz Uwe
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Stadt Seeland, Germany. scholz@ipk-gatersleben.de.
Waugh Robbie
Division of Plant Sciences, University of Dundee & The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK. Robbie.Waugh@hutton.ac.uk.
Poland Jesse A
Department of Plant Pathology, Kansas State University, Manhattan, KS, 65506, USA. jpoland@ksu.edu.
Muehlbauer Gary J
Departments of Agronomy and Plant Genetics, and Plant Biology, University of Minnesota, St Paul, MN, 55108, USA. muehl003@umn.edu.
Stein Nils
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Stadt Seeland, Germany. stein@ipk-gatersleben.de.
Rokhsar Daniel S
Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA. dsrokhsar@gmail.com. | Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA. dsrokhsar@gmail.com.
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Article Info
Journal
Genome biology
Abbr.
Genome Biol
ISSN
1474-760X
DOI
10.1186/s13059-015-0582-8
Email
jarrodc@gmail.com
mascher@ipk-gatersleben.de
abuluc@lbl.gov
kwbarry@lbl.gov
egeor@eecs.berkeley.edu
adamsession@berkeley.edu
veronika@cs.ucsb.edu
jjenkins@hudsonalpha.org
sunish.sehgal@sdstate.edu
loliker@lbl.gov
jschmutz@hudsonalpha.org
yelick@eecs.berkeley.edu
scholz@ipk-gatersleben.de
robbie.waugh@hutton.ac.uk
jpoland@ksu.edu
muehl003@umn.edu
stein@ipk-gatersleben.de
dsrokhsar@gmail.com
Published
2015-01-31
Epub
2015-00-31
Pages
26
Language
English
Region
England
NLM ID
100960660
PMCID
PMC4373400
Subset
IM
Grants
Biotechnology and Biological Sciences Research Council · BB/I00663X/1 · United Kingdom
External Links
PubMed source DOI: 10.1186/s13059-015-0582-8 PMC Full Text View journal details
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