Assessing Illumina and Velvet for sequencing and assembling a wheat chromosome arm

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Recent major advances in sequencing technology provide a timely opportunity to devise new sequencing strategies to tackle large and complex genomes that to date have been impracticable and unjustifiably expensive to sequence. We aim to assess the Illumina sequencing platform for generating transcriptome, BAC and genomic sequence of wheat, which has an extremely large (16 Gbp) hexaploid genome. The Illumina GA2 platform provides an excellent cost- effective sequence throughput that is continually being improved in terms of sequencing chemistry and base-calling. Although the GS-FLX Titanium system generates substantially longer read lengths, its cost per base is sufficiently higher than that of the Illumina platform to make the judgement that continued improvements in the Illumina platform will be adequate for generating sequence to sufficient depth for useful assembly of long contigs covering the low copy regions of wheat chromosomes. Once developed, these very cost- effective applications will be more readily taken up by the research community and applied for the rapid generation of wheat genome sequences. We also aim to develop specific computational and mathematical approaches to assemble and analyse wheat transcriptome and genome sequence. The outcomes of the proposed work will provide strategies for the cost effective sequencing of the complete wheat genome and for the compilation and analysis of the sequence into useful assemblies. Furthermore, strategies for targeting re-sequencing to gene-rich regions of the wheat genome will facilitate genotyping and association genetics studies in multiple commercial breeding lines.

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