Sequencing wheat chromosome arm 7BS delimits the 7BS/4AL translocation and reveals homoeologous gene conservation

Berkman, Paul J., Skarshewski, Adam, Manoli, Sahana, Lorenc, Michal T., Stiller, Jiri, Smits, Lars, Lai, Kaitao, Campbell, Emma, Kubalakova, Marie, Simkova, Hana, Batley, Jacqueline, Dolezel, Jaroslav, Hernandez, Pilar and Edwards, David (2012) Sequencing wheat chromosome arm 7BS delimits the 7BS/4AL translocation and reveals homoeologous gene conservation. Theoretical and Applied Genetics, 124 3: 423-432. doi:10.1007/s00122-011-1717-2


Author Berkman, Paul J.
Skarshewski, Adam
Manoli, Sahana
Lorenc, Michal T.
Stiller, Jiri
Smits, Lars
Lai, Kaitao
Campbell, Emma
Kubalakova, Marie
Simkova, Hana
Batley, Jacqueline
Dolezel, Jaroslav
Hernandez, Pilar
Edwards, David
Title Sequencing wheat chromosome arm 7BS delimits the 7BS/4AL translocation and reveals homoeologous gene conservation
Journal name Theoretical and Applied Genetics   Check publisher's open access policy
ISSN 0040-5752
1432-2242
Publication date 2012-02-01
Year available 2011
Sub-type Article (original research)
DOI 10.1007/s00122-011-1717-2
Open Access Status Not Open Access
Volume 124
Issue 3
Start page 423
End page 432
Total pages 10
Place of publication Heidelberg, Germany
Publisher Springer
Language eng
Subject 1305 Biotechnology
1102 Agronomy and Crop Science
1311 Genetics
Abstract Complex Triticeae genomes pose a challenge to genome sequencing efforts due to their size and repetitive nature. Genome sequencing can reveal details of conservation and rearrangements between related genomes. We have applied Illumina second generation sequencing technology to sequence and assemble the low copy and unique regions of Triticum aestivum chromosome arm 7BS, followed by the construction of a syntenic build based on gene order in Brachypodium. We have delimited the position of a previously reported translocation between 7BS and 4AL with a resolution of one or a few genes and report approximately 13% genes from 7BS having been translocated to 4AL. An additional 13 genes are found on 7BS which appear to have originated from 4AL. The gene content of the 7DS and 7BS syntenic builds indicate a total of ~77,000 genes in wheat. Within wheat syntenic regions, 7BS and 7DS share 740 genes and a common gene conservation rate of ~39% of the genes from the corresponding regions in Brachypodium, as well as a common rate of colinearity with Brachypodium of ~60%. Comparison of wheat homoeologues revealed ~84% of genes previously identified in 7DS have a homoeologue on 7BS or 4AL. The conservation rates we have identified among wheat homoeologues and with Brachypodium provide a benchmark of homoeologous gene conservation levels for future comparative genomic analysis. The syntenic build of 7BS is publicly available at http://www.wheatgenome.info.
Formatted abstract
Complex Triticeae genomes pose a challenge to genome sequencing efforts due to their size and repetitive nature. Genome sequencing can reveal details of conservation and rearrangements between related genomes. We have applied Illumina second generation sequencing technology to sequence and assemble the low copy and unique regions of Triticum aestivum chromosome arm 7BS, followed by the construction of a syntenic build based on gene order in Brachypodium. We have delimited the position of a previously reported translocation between 7BS and 4AL with a resolution of one or a few genes and report approximately 13% genes from 7BS having been translocated to 4AL. An additional 13 genes are found on 7BS which appear to have originated from 4AL. The gene content of the 7DS and 7BS syntenic builds indicate a total of ~77,000 genes in wheat. Within wheat syntenic regions, 7BS and 7DS share 740 genes and a common gene conservation rate of ~39% of the genes from the corresponding regions in Brachypodium, as well as a common rate of colinearity with Brachypodium of ~60%. Comparison of wheat homoeologues revealed ~84% of genes previously identified in 7DS have a homoeologue on 7BS or 4AL. The conservation rates we have identified among wheat homoeologues and with Brachypodium provide a benchmark of homoeologous gene conservation levels for future comparative genomic analysis. The syntenic build of 7BS is publicly available at http://www.wheatgenome.info.
Keyword Polyploid wheat
Bin map
Brachypodium-distachyon
Plant genomes
Q-Index Code C1
Q-Index Status Confirmed Code
Grant ID LP0882095
LC06004
CZ.1.05/2.1.00/01.0007
BIO2009-07443
Institutional Status UQ
Additional Notes Published online: 15 October 2011

 
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Created: Sun, 16 Oct 2011, 05:04:00 EST by Dr Dave Edwards on behalf of Qld Alliance for Agriculture and Food Innovation