7A Survey Sequencing
Targeted chromosomes
|
Project team
| First name | Last name | Institution | Country | |
|---|---|---|---|---|
| David | Edwards | Dave.EdwardsSPAMFILTER@uq.edu.au | ACPFG-University of Queensland | Australia |
| Paul | Berkman | p.berkmanSPAMFILTER@uq.edu.au | ACPFG-University of Queensland | Australia |
| Sahana | Manoli | University of Queensland | Australia | |
| Michael | Lorenc | ACPFG-University of Queensland | Australia | |
| Jiri | Stiller | University of Queensland | Australia | |
| Lars | Smits | University of Queensland | Australia | |
| Kaitao | Lai | ACPFG-University of Queensland | Australia | |
| Paul | Visendi | ACPFG-University of Queensland | Australia | |
| Pradeep | Ruperao | University of Queensland | Australia | |
| Hong | Lee | University of Queensland | Australia | |
| Jacqueline | Batley | University of Queensland | Australia | |
| Emma | Campbell | University of Queensland | Australia |
Project collaborators
| First name | Last name | Institution | Country | |
|---|---|---|---|---|
| Jaroslav | Dolezel | dolezelSPAMFILTER@ueb.cas.cz | IEB | Czech Republic |
| Hana | Šimková | simkovahSPAMFILTER@ueb.cas.cz | IEB | Czech Republic |
| Marie | Kubaláková | mariekSPAMFILTER@ueb.cas.cz | IEB | Czech Republic |
| Peter | Langridge | Peter.langridgeSPAMFILTER@acpfg.com.au | ACPFG | Australia |
| Delphine | Fleury | delphine.fleurySPAMFILTER@acpfg.com.au | ACPFG | Australia |
Project funding
Funding for the 7A survey sequencing project has been provided by the Australian Research Council on two grants: an ARC Linkage grant (LP0882095) awarded to Dave Edwards “Developing technology for the cost effective de novo sequencing and analysis of complex genomes”, and an International Science Linkage grant awarded to Delphine Fleury and Peter Langridge “Genomics for Triticeae improvement for food, feed and non-food uses“ linked to the FP7 European project TriticeaeGenome. Additional DNA sequence data was provided by Bioplatforms Australia.
Abstract
The project aims to shot-gun sequence and assemble the complete gene content and low copy regions of the chromosome 7A of Chinese Spring using the method detailed in ( Berkman et al. 2011a , Berkman et al. 2011b ). The DNA was purified and amplified by Jaroslav Dolezel’s group. Libraries were generated by the group of Jacqueline Batley and sequenced by the Australian Genome Research Facility (AGRF). The coverage was 35x and 50x for short and long arms, respectively. Sequence assembly, generation of a syntenic build and annotation was undertaken by the Edwards group. Annotated assemblies are hosted freely on a GBrowse database at www.wheatgenome.info ( Lai et al. 2011 ).
The data will be aligned with the physical map of chromosome 7A, project funded by Grain Research and Development Council.
Publications
Berkman, B.J., Skarshewski, A., Lorenc, M.T., Lai, K., Duran, C., Ling, E.Y.S., Stiller, J., Smits, L., Imelfort, M., Manoli, S., McKenzie, M., Kubalakova, M., Simkova, H., Batley, J., Fleury, D., Dolezel, J. and Edwards, D. (2011) Sequencing and assembly of low copy and genic regions of isolated Triticum aestivum chromosome arm 7DS. Plant Biotechnology Journal , 9, 768-775.
Berkman, P.J., Skarshewski, A., Manoli, S., Lorenc, M.T., Stiller, J., Lars, Smits, L., Lai, K., Campbell, E., Kubalakova, M., Simkova, H., Batley, J., Dolezel, J., Hernandez, P. and Edwards, D. (2012) Sequencing wheat chromosome arm 7BS delimits the 7BS/4AL translocation and reveals homoeologous gene conservation. Theoretical and Applied Genetics , 124(3):423-32. Doi: 10.1007/s00122-011-1717.2. Epub 2011 Oct.15.