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

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 hexapl...

Descripción completa

Detalles Bibliográficos
Autores principales: Chapman, Jarrod A, Mascher, Martin, Buluç, Aydın, 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
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2015
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4373400/
https://www.ncbi.nlm.nih.gov/pubmed/25637298
http://dx.doi.org/10.1186/s13059-015-0582-8
_version_ 1782363335153418240
author Chapman, Jarrod A
Mascher, Martin
Buluç, Aydın
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
author_facet Chapman, Jarrod A
Mascher, Martin
Buluç, Aydın
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
author_sort Chapman, Jarrod A
collection PubMed
description 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-015-0582-8) contains supplementary material, which is available to authorized users.
format Online
Article
Text
id pubmed-4373400
institution National Center for Biotechnology Information
language English
publishDate 2015
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-43734002015-03-26 A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome Chapman, Jarrod A Mascher, Martin Buluç, Aydın 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 Genome Biol Method 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-015-0582-8) contains supplementary material, which is available to authorized users. BioMed Central 2015-01-31 2015 /pmc/articles/PMC4373400/ /pubmed/25637298 http://dx.doi.org/10.1186/s13059-015-0582-8 Text en © Chapman et al.; licensee BioMed Central. 2015 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Method
Chapman, Jarrod A
Mascher, Martin
Buluç, Aydın
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
title A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome
title_full A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome
title_fullStr A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome
title_full_unstemmed A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome
title_short A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome
title_sort whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4373400/
https://www.ncbi.nlm.nih.gov/pubmed/25637298
http://dx.doi.org/10.1186/s13059-015-0582-8
work_keys_str_mv AT chapmanjarroda awholegenomeshotgunapproachforassemblingandanchoringthehexaploidbreadwheatgenome
AT maschermartin awholegenomeshotgunapproachforassemblingandanchoringthehexaploidbreadwheatgenome
AT bulucaydın awholegenomeshotgunapproachforassemblingandanchoringthehexaploidbreadwheatgenome
AT barrykerrie awholegenomeshotgunapproachforassemblingandanchoringthehexaploidbreadwheatgenome
AT georganasevangelos awholegenomeshotgunapproachforassemblingandanchoringthehexaploidbreadwheatgenome
AT sessionadam awholegenomeshotgunapproachforassemblingandanchoringthehexaploidbreadwheatgenome
AT strnadovaveronika awholegenomeshotgunapproachforassemblingandanchoringthehexaploidbreadwheatgenome
AT jenkinsjerry awholegenomeshotgunapproachforassemblingandanchoringthehexaploidbreadwheatgenome
AT sehgalsunish awholegenomeshotgunapproachforassemblingandanchoringthehexaploidbreadwheatgenome
AT olikerleonid awholegenomeshotgunapproachforassemblingandanchoringthehexaploidbreadwheatgenome
AT schmutzjeremy awholegenomeshotgunapproachforassemblingandanchoringthehexaploidbreadwheatgenome
AT yelickkatherinea awholegenomeshotgunapproachforassemblingandanchoringthehexaploidbreadwheatgenome
AT scholzuwe awholegenomeshotgunapproachforassemblingandanchoringthehexaploidbreadwheatgenome
AT waughrobbie awholegenomeshotgunapproachforassemblingandanchoringthehexaploidbreadwheatgenome
AT polandjessea awholegenomeshotgunapproachforassemblingandanchoringthehexaploidbreadwheatgenome
AT muehlbauergaryj awholegenomeshotgunapproachforassemblingandanchoringthehexaploidbreadwheatgenome
AT steinnils awholegenomeshotgunapproachforassemblingandanchoringthehexaploidbreadwheatgenome
AT rokhsardaniels awholegenomeshotgunapproachforassemblingandanchoringthehexaploidbreadwheatgenome
AT chapmanjarroda wholegenomeshotgunapproachforassemblingandanchoringthehexaploidbreadwheatgenome
AT maschermartin wholegenomeshotgunapproachforassemblingandanchoringthehexaploidbreadwheatgenome
AT bulucaydın wholegenomeshotgunapproachforassemblingandanchoringthehexaploidbreadwheatgenome
AT barrykerrie wholegenomeshotgunapproachforassemblingandanchoringthehexaploidbreadwheatgenome
AT georganasevangelos wholegenomeshotgunapproachforassemblingandanchoringthehexaploidbreadwheatgenome
AT sessionadam wholegenomeshotgunapproachforassemblingandanchoringthehexaploidbreadwheatgenome
AT strnadovaveronika wholegenomeshotgunapproachforassemblingandanchoringthehexaploidbreadwheatgenome
AT jenkinsjerry wholegenomeshotgunapproachforassemblingandanchoringthehexaploidbreadwheatgenome
AT sehgalsunish wholegenomeshotgunapproachforassemblingandanchoringthehexaploidbreadwheatgenome
AT olikerleonid wholegenomeshotgunapproachforassemblingandanchoringthehexaploidbreadwheatgenome
AT schmutzjeremy wholegenomeshotgunapproachforassemblingandanchoringthehexaploidbreadwheatgenome
AT yelickkatherinea wholegenomeshotgunapproachforassemblingandanchoringthehexaploidbreadwheatgenome
AT scholzuwe wholegenomeshotgunapproachforassemblingandanchoringthehexaploidbreadwheatgenome
AT waughrobbie wholegenomeshotgunapproachforassemblingandanchoringthehexaploidbreadwheatgenome
AT polandjessea wholegenomeshotgunapproachforassemblingandanchoringthehexaploidbreadwheatgenome
AT muehlbauergaryj wholegenomeshotgunapproachforassemblingandanchoringthehexaploidbreadwheatgenome
AT steinnils wholegenomeshotgunapproachforassemblingandanchoringthehexaploidbreadwheatgenome
AT rokhsardaniels wholegenomeshotgunapproachforassemblingandanchoringthehexaploidbreadwheatgenome

Ejemplares similares