Sequencing and assembly of low copy and genic regions of isolated Triticum aestivum chromosome arm 7DS

Berkman, Paul J., Skarshewski, Adam, Lorenc, Michal T., Lai, Kaitao, Duran, Chris, Ling, Edmund Y. S., Stiller, Jiri, Smits, Lars, Imelfort, Michael, Manoli, Sahana, McKenzie, Megan, Kubalakova, Marie, Simkova, Hana, Batley, Jacqueline, Fleury, Delphine, Dolezel, Jaroslav and Edwards, David (2011) Sequencing and assembly of low copy and genic regions of isolated Triticum aestivum chromosome arm 7DS. Plant Biotechnology Journal, 9 7: 768-775. doi:10.1111/j.1467-7652.2010.00587.x


Author Berkman, Paul J.
Skarshewski, Adam
Lorenc, Michal T.
Lai, Kaitao
Duran, Chris
Ling, Edmund Y. S.
Stiller, Jiri
Smits, Lars
Imelfort, Michael
Manoli, Sahana
McKenzie, Megan
Kubalakova, Marie
Simkova, Hana
Batley, Jacqueline
Fleury, Delphine
Dolezel, Jaroslav
Edwards, David
Title Sequencing and assembly of low copy and genic regions of isolated Triticum aestivum chromosome arm 7DS
Formatted title
Sequencing and assembly of low copy and genic regions of isolated Triticum aestivum chromosome arm 7DS
Journal name Plant Biotechnology Journal   Check publisher's open access policy
ISSN 1467-7644
1467-7652
Publication date 2011-09-01
Year available 2011
Sub-type Article (original research)
DOI 10.1111/j.1467-7652.2010.00587.x
Open Access Status DOI
Volume 9
Issue 7
Start page 768
End page 775
Total pages 8
Place of publication Hants, United Kingdom
Publisher Wiley-Blackwell Publishing
Language eng
Abstract The genome of bread wheat (Triticum aestivum) is predicted to be greater than 16 Gbp in size and consist predominantly of repetitive elements, making the sequencing and assembly of this genome a major challenge. We have reduced genome sequence complexity by isolating chromosome arm 7DS and applied second-generation technology and appropriate algorithmic analysis to sequence and assemble low copy and genic regions of this chromosome arm. The assembly represents approximately 40% of the chromosome arm and all known 7DS genes. Comparison of the 7DS assembly with the sequenced genomes of rice (Oryza sativa) and Brachypodium distachyon identified large regions of conservation. The syntenic relationship between wheat, B. distachyon and O. sativa, along with available genetic mapping data, has been used to produce an annotated draft 7DS syntenic build, which is publicly available at http://www.wheatgenome.info. Our results suggest that the sequencing of isolated chromosome arms can provide valuable information of the gene content of wheat and is a step towards whole-genome sequencing and variation discovery in this important crop.
Formatted abstract
The genome of bread wheat (Triticum aestivum) is predicted to be greater than 16 Gbp in size and consist predominantly of repetitive elements, making the sequencing and assembly of this genome a major challenge. We have reduced genome sequence complexity by isolating chromosome arm 7DS and applied second-generation technology and appropriate algorithmic analysis to sequence and assemble low copy and genic regions of this chromosome arm. The assembly represents approximately 40% of the chromosome arm and all known 7DS genes. Comparison of the 7DS assembly with the sequenced genomes of rice (Oryza sativa) and Brachypodium distachyon identified large regions of conservation. The syntenic relationship between wheat, B. distachyon and O. sativa, along with available genetic mapping data, has been used to produce an annotated draft 7DS syntenic build, which is publicly available at http://www.wheatgenome.info. Our results suggest that the sequencing of isolated chromosome arms can provide valuable information of the gene content of wheat and is a step towards whole-genome sequencing and variation discovery in this important crop.
Keyword Wheat genome sequence
Chromosome 7
Genome assembly
Gene annotation
Q-Index Code C1
Q-Index Status Confirmed Code
Grant ID LP0882095
521/07/1573
ED0007/01/01
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Centre for Integrative Legume Research Publications
Official 2012 Collection
School of Agriculture and Food Sciences
 
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