Shotgun sequencing and targeted enrichment of sugarcane genome sequences

Even though the genome of sugarcane is scientifically challenging due to its large size and complexity, it has been feasible to study using conventional tools such as genetic linkage maps made from DNA markers and to produce BAC libraries - albeit with relatively low overall coverage. We have carried out second generation sequencing using paired end reads (Illumina GA IIx, 76 bp) of whole genome shotgun (WGS) libraries to determine what can be mined from this information. From assembly to a sugarcane chloroplast reference sequence, it has been possible to determine the sequence of chloroplast genomes from WGS and to compare chloroplast sequences from different Saccharum species. The nature and relative abundance of repetitive elements using de novo assembly of these short reads has also been possible. In addition, regions of homology with Sorghum can be identified by direct alignment of WGS reads with Sorghum genes. To uncover polymorphisms in selected genes, which could be mapped and potentially linked to function, we have undertaken targeted enrichment of the sugarcane WGS libraries from the parents of a mapping population (PJ2). The Agilent SureSelect system was used to provide baits for hybridisation with the design of most probes based on predicted coding sequence from the genome sequence of Sorghum. The depth of sequence obtained will enable the detection of likely candidate single dose SNPs and indels for informative genotyping for mapping on the Q165 linkage map.