LoCoLotive: In silico mining for low-copy nuclear loci based on target capture probe sets and arbitrary reference genomes.

Abstract

Universal target enrichment probe kits are used to circumvent the individual identification of loci suitable for phylogenetic studies in a given taxon. Under certain circumstances, however, target capture can be inefficient and costly, and lower numbers of marker loci may be sufficient. We therefore propose a computational pipeline that enables the easy identification of a subset of promising candidate loci for a taxon of interest. Target sequences used for probe design are filtered based on an assembled reference genome, resulting in presumably intron-containing single-copy loci as present in the reference taxon. The applicability of the proposed approach is demonstrated based on two probe kits (universal and family-specific) in combination with several publicly available reference genomes. Guided by commercial probe kits, LoCoLotive enables fast and cost-efficient marker mining. Its accuracy mainly depends on the quality of the reference genome and its relatedness to the taxa under study.