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Title

From small and simple to big and complex: what can short sequence reads tell us about genomes?

AuthorsLorenc, Michal; Hernández Molina, Pilar ; Edwards, David
Issue DateAug-2011
Citation21st Annual Combined Biological Sciences Meeting (2011)
AbstractFrom small and simple to big and complex: what can short sequence reads tell us about genomes? Michal Lorenc, Kaitao Lai, Paul Berkman, Kenneth Chan, Mike Imelfort, Sahana Manoli, Chris Duran, Hong Lee, Edmund Ling, Hana Šimková, Marie Kubaláková, Emma Campbell, Pilar Hernandez, Jacqueline Batley, Jiri Stiller, Jaroslav Doležel and David Edwards The genome sequence of an organism provides the bas is for gene discovery, the analysis of genetic variation and the association of genomic variation with heritable traits. Second generation sequencing technologies and applied bioinformatics tools can provide an unprecedented insight into genome structure and variation. This technology is still in its infancy, yet is already making a huge impact in our understanding of biological processes. We have developed and applied novel bioinformatics tools and approaches for Illumina second generation sequence data analysis with the aim of understanding large and complex genomes. The genome of bread wheat (Triticum aestivum) is greater than 16 Gbp in size and consists predominantly of repetitive element s. There has been some debate over whether second generation sequencing can be applied for such a large and complex genome. We have reduced genome sequence complexity by sequencing isolated chromosome arms, with the aim to assemble low copy and genic regions. Our approach enabled the assembly of all genes, as well as a substantial portion of the repetitive fraction for these chromosome s. The syntenic relationship between wheat and a sequenced close relative, Brachypodium distachyon has been used to produce annotated syntenic builds, whereby the majority of genes have been placed in an approximate order and orientation. Our results suggest that the sequencing of isolated chromosome arms can provide valuable information on the gene content of wheat, and that these assemblies can be applied for genome wide SNP discovery, the identification of candidate genes associated with genetically mapped traits and investigation of genome evolution in this important crop. Our research in canola (Brassica napus) is more advanced and we have identified more than 1 million SNPs across the polyploid genome, with a validat ion accuracy of 96%. This information has been integrated with mapped genetic marker and trait information within searchable databases. The resulting tools enable the association of candidat e genes with trait associated genetic markers and the study of Brassica genome evolution under select ion. Our results demonstrate that the challenges of analysing very large and complex genomes using short read sequences are at least partially overcome and that this technology has the potential to revolutionise our understanding of crop genomes with applications for future crop improvement.
DescriptionLorenc, Michal et al.-- Ponencia presentada en la 21st Annual Combined Biological Sciences Meeting, celebrada en Australia el 26 de agosto de 2011.
URIhttp://hdl.handle.net/10261/97167
Appears in Collections:(IAS) Comunicaciones congresos
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