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

ABSTRACT:

Premise

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.

Methods and results

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

SUBMITTER: Lautenschlager U 

PROVIDER: S-EPMC10719872 | biostudies-literature | 2023 Nov-Dec

REPOSITORIES: biostudies-literature