title: A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome.
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.
authors: Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA. jarrodc@gmail.com.
authors: Jarrod A
authors: JA
authors: Chapman
authors: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Stadt Seeland, Germany. mascher@ipk-gatersleben.de.
authors: Martin
authors: M
authors: Mascher
authors: Computational Research Division and National Energy Research Supercomputing Center (NERSC), Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. abuluc@lbl.gov.
authors: Aydın
authors: A
authors: Buluç
authors: Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA. kwbarry@lbl.gov.
authors: Kerrie
authors: K
authors: Barry
authors: 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.
authors: Evangelos
authors: E
authors: Georganas
authors: Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA. adamsession@berkeley.edu.
authors: Adam
authors: A
authors: Session
authors: Department of Computer Science, University of California, Santa Barbara, CA, 93106, USA. veronika@cs.ucsb.edu.
authors: Veronika
authors: V
authors: Strnadova
authors: 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.
authors: Jerry
authors: J
authors: Jenkins
authors: 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.
authors: Sunish
authors: S
authors: Sehgal
authors: Computational Research Division and National Energy Research Supercomputing Center (NERSC), Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. loliker@lbl.gov.
authors: Leonid
authors: L
authors: Oliker
authors: 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.
authors: Jeremy
authors: J
authors: Schmutz
authors: 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.
authors: Katherine A
authors: KA
authors: Yelick
authors: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Stadt Seeland, Germany. scholz@ipk-gatersleben.de.
authors: Uwe
authors: U
authors: Scholz
authors: Division of Plant Sciences, University of Dundee & The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK. Robbie.Waugh@hutton.ac.uk.
authors: Robbie
authors: R
authors: Waugh
authors: Department of Plant Pathology, Kansas State University, Manhattan, KS, 65506, USA. jpoland@ksu.edu.
authors: Jesse A
authors: JA
authors: Poland
authors: Departments of Agronomy and Plant Genetics, and Plant Biology, University of Minnesota, St Paul, MN, 55108, USA. muehl003@umn.edu.
authors: Gary J
authors: GJ
authors: Muehlbauer
authors: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Stadt Seeland, Germany. stein@ipk-gatersleben.de.
authors: Nils
authors: N
authors: Stein
authors: 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.
authors: Daniel S
authors: DS
authors: Rokhsar
mesh_terms: D001939:Bread; D002874:Chromosome Mapping; D020451:Contig Mapping; D018076:DNA, Complementary / Q000235:genetics; D008040:Genetic Linkage; D014644:Genetic Variation; D018745:Genome, Plant; D006720:Homozygote; D009711:Nucleotides / Q000235:genetics; D011123:Polyploidy; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA / Q000379:methods*; D014908:Triticum / Q000235:genetics*
chemical_list: D018076:DNA, Complementary; D009711:Nucleotides
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