Second generation sequencing and analysis of complex genomes

Abstract

The genome sequence of an organism provides the basis 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 complex genomes. These range from large genome polyploid crops such as wheat and Brassica species, to complex environmental metagenomic samples. For crop genomes, we aim to identify genes, novel and mapped genetic markers and develop methods for the association of agronomic traits with underlying genomic variation. In canola (Brassica napus) we have identified more than 1 million SNPs across the polyploid genome, with a validation 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 candidate genes with trait associated genetic markers and the study of Brassica genome evolution under selection. The genome of bread wheat (Triticum aestivum) is greater than 16 Gbp in size and consists predominantly of repetitive elements. 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. 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. Finally, as an example of second generation metagenome bioinformatics, I will describe approaches to understand the complex coral holobiont and its response to environmental change, a study which is challenged by a lack of reference genomes or even knowledge of which species are present in the sample.