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

Abstract

We report that 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:
 [1];  [2];  [3];  [1];  [4];  [5];  [5];  [6];  [7];  [3];  [6];  [4];  [2];  [8];  [9];  [10];  [2];  [11]
  1. Department of Energy Joint Genome Institute, Walnut Creek, CA (United States)
  2. Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben (Germany)
  3. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  4. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States)
  5. Univ. of California, Berkeley, CA (United States)
  6. Department of Energy Joint Genome Institute, Walnut Creek, CA (United States); HudsonAlpha Institute of Biotechnology, Huntsville, AL (United States)
  7. Kansas State Univ., Manhattan, KS (United States); South Dakota State Univ., Brookings, SD (United States)
  8. Univ. of Dundee & The James Hutton Institute, Dundee (United Kingdom)
  9. Kansas State Univ., Manhattan, KS (United States)
  10. Univ. of Minnesota, St. Paul, MN (United States)
  11. Department of Energy Joint Genome Institute, Walnut Creek, CA (United States); Univ. of California, Berkeley, CA (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1256489
Grant/Contract Number:
AC02-05CH11231; SC0008700
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Genome Biology
Additional Journal Information:
Journal Volume: 16; Journal Issue: 1; Journal ID: ISSN 1465-6906
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Chapman, Jarrod A., Mascher, Martin, Buluc, Aydin, Barry, Kerrie, Georganas, Evangelos, Session, Adam, Strnadova, Veronika, Jenkins, Jerry, Sehgal, Sunish, Oliker, Leonid, Schmutz, Jeremy, Yelick, Katherine A., Scholz, Uwe, Waugh, Robbie, Poland, Jesse A., Muehlbauer, Gary J., Stein, Nils, and Rokhsar, Daniel S. A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome. United States: N. p., 2015. Web. doi:10.1186/s13059-015-0582-8.
Chapman, Jarrod A., Mascher, Martin, Buluc, Aydin, Barry, Kerrie, Georganas, Evangelos, Session, Adam, Strnadova, Veronika, Jenkins, Jerry, Sehgal, Sunish, Oliker, Leonid, Schmutz, Jeremy, Yelick, Katherine A., Scholz, Uwe, Waugh, Robbie, Poland, Jesse A., Muehlbauer, Gary J., Stein, Nils, & Rokhsar, Daniel S. A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome. United States. doi:10.1186/s13059-015-0582-8.
Chapman, Jarrod A., Mascher, Martin, Buluc, Aydin, Barry, Kerrie, Georganas, Evangelos, Session, Adam, Strnadova, Veronika, Jenkins, Jerry, Sehgal, Sunish, Oliker, Leonid, Schmutz, Jeremy, Yelick, Katherine A., Scholz, Uwe, Waugh, Robbie, Poland, Jesse A., Muehlbauer, Gary J., Stein, Nils, and Rokhsar, Daniel S. Sat . "A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome". United States. doi:10.1186/s13059-015-0582-8. https://www.osti.gov/servlets/purl/1256489.
@article{osti_1256489,
title = {A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome},
author = {Chapman, Jarrod A. and Mascher, Martin and Buluc, Aydin and Barry, Kerrie and Georganas, Evangelos and Session, Adam and Strnadova, Veronika and Jenkins, Jerry and Sehgal, Sunish and Oliker, Leonid and Schmutz, Jeremy and Yelick, Katherine A. and Scholz, Uwe and Waugh, Robbie and Poland, Jesse A. and Muehlbauer, Gary J. and Stein, Nils and Rokhsar, Daniel S.},
abstractNote = {We report that 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.},
doi = {10.1186/s13059-015-0582-8},
journal = {Genome Biology},
number = 1,
volume = 16,
place = {United States},
year = {Sat Jan 31 00:00:00 EST 2015},
month = {Sat Jan 31 00:00:00 EST 2015}
}

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