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5D 454 Survey Sequencing

Targeted chromosomes

5D
5D
Click on a chromosome to access associated data (when available) at URGI Sequences Repository.

Project team

First nameLast nameEmailInstitutionCountry
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 nameLast nameEmailInstitutionCountry
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