5D 454 Survey Sequencing
Targeted chromosomes
|
Project team
| First name | Last name | Institution | Country | |
|---|---|---|---|---|
| Stuart James | Lucas | slucasSPAMFILTER@sabanciuniv.edu | Sabanci University | Turkey |
| Zohar | Weinstein | Sabanci University | Turkey | |
| Fatme | Aydinoglu | Sabanci University | Turkey | |
| Ani | Akpinar | Sabanci University | Turkey |
Project collaborators
| First name | Last name | Institution | Country | |
|---|---|---|---|---|
| Jane | Rogers | Jane.RogersSPAMFILTER@bbsrc.ac.uk | The Genome Analysis Centre | United Kingdom |
Project funding
Funding for Roche 454 sequencing was provided by Sabanci University, Istanbul, Turkey.
Abstract
Shotgun sequence reads were generated from each arm of flow sorted chromosome 5D using Roche 454 FLX Titanium technology. Using similarity and assembly-based methods 1.34x and 1.61x coverage of the short (5DS) and long (5DL) arms of the chromosome were analysed to identify 1314 (5DS) and 2975 (5DL) coding sequence models. Approximately 74% of the reads represented repetitive elements. The data were integrated with 518 wheat markers and guided by synteny to generate a virtual gene order which revealed a large rearrangement in the peri-centromeric region and a high density of non-syntenic genes in the telomeric region of 5DS.
Data accession
Sequence data have been deposited in the EBI European Nucleotide Archive, Study no. ERP002330.
Publications
- Lucas SJ, Akpınar BA, Šimková H, Kubaláková M, Doležel J, Budak H. Next-generation sequencing of flow-sorted wheat chromosome 5D reveals lineage-specific translocations and widespread gene duplications. BMC Genomics. 2014 Dec 9;15:1080. doi: 10.1186/1471-2164-15-1080.
- Kurtoglu KY, Kantar M, Lucas SJ, Budak H. Unique and conserved microRNAs in wheat chromosome 5D revealed by next-generation sequencing. PLoS One. 2013 Jul 23;8(7):e69801. doi: 10.1371/journal.pone.0069801.