Characterising Genome Structural Variation Using Illumina Next Generation DNA Sequencing

Illumina second generation sequencing technologies and applied bioinformatics tools can provide an unprecedented insight into genome structure, variation and function. 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 data analysis with the aim of understanding structural variation between species and individuals.

Using a skim based genotyping-by-sequencing method, combined with the sequencing of isolated chromosomes, we have identified differences in genome structure between individuals and reference genomes. This approach can be applied to identify structural variation, the introgression of alien DNA, transgenes as well as assembly errors in reference genomes. Examples will be presented from wheat, Brassica and chickpea, but the approach is broadly applicable to a range of species.