Targeting Genomic Regions of Interest in Non-Model Organisms

Targeted enrichment enables the sequencing of low-copy genomic regions, from SNPs to long loci, and can be applied to pools containing many samples. Combined with a genome skimming approach, sequenced pools may additionally allow assembly of non-targeted high-copy genomic regions, such as the mitochondrial, chloroplast, and nuclear ribosomal regions. Targeted enrichment requires some prior knowledge of the regions to be targeted, knowledge that is often lacking in non-model organisms. However, published resources from related organisms, or preliminary genomic or transcriptomic data can be used for probe development. We describe workflows for developing target loci for non-model organisms from genomic or transcriptomic data, for both SNPs and longer loci, and discuss methods of organizing raw sequence data into reconstructed loci for many samples. Additional topics include pros and cons of target enrichment compared to restriction digest techniques, capturing non-targeted high-copy regions, and considerations for pooling multiple samples.