Genome wide SNP detection in the great tit Parus major using high throughput sequencing

Next generation sequencing technologies have dramatically lowered the costs to obtain genomic sequence information. This has opened exiting possibilities for (partial) de novo assembly of genomes, and for genome-wide SNP detection in organisms currently lacking a sequenced genome. We have combined high throughput sequencing (Illumina GA) with de novo assembly of the resulting short reads into small contigs. These contigs function as a reference sequence for mapping of the original short sequence reads, allowing the detection of high quality SNPs. The contig sequence provides the flanking sequence essential for use in a genotyping assay. This strategy has resulted in the detection of more than 7,000 novel SNPs in turkey (Meleagris gallopavo), 3,500 SNPs in tilapia (Oreochromis niloticus), and over 20,000 SNPs for the ecological model species Parus major, the great tit. Mapping of the contig sequences against the genome sequence of a related species, e.g. chicken in case of turkey and the zebra finch in case of the great tit, allows the selection of genome-wide distributed SNPs. Additionally, the availability of the genome sequence of a related species can be employed for the merging of adjacent contigs, which increases the number of SNPs usable in a genotyping assay.