SNP Discovery in Non-model Organisms Using 454 Next Generation Sequencing

Roche 454 sequencing of the transcriptome has become a standard approach for efficiently obtaining single nucleotide polymorphisms (SNPs) in non-model species. In this chapter, the primary issues facing the development of SNPs from the transcriptome in non-model species are presented: tissue and sampling choices, mRNA preparation, considerations of normalization, pooling and barcoding, how much to sequence, how to assemble the data and assess the assembly, calling transcriptome SNPs, developing these into genomic SNPs, and publishing the work. Discussion also covers the comparison of this approach to RAD-tag sequencing and the potential of using other sequencing platforms for SNP development.