Dataset Information
LoCoLotive: In silico mining for low-copy nuclear loci based on target capture probe sets and arbitrary reference genomes.
Ontology highlight
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 several publicly available reference genomes.Conclusions
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.
SUBMITTER: Lautenschlager U
PROVIDER: S-EPMC10719872 | biostudies-literature | 2023 Nov-Dec
REPOSITORIES: biostudies-literature
Publications
LoCoLotive: In silico mining for low-copy nuclear loci based on target capture probe sets and arbitrary reference genomes.
Applications in plant sciences 20230728 6
<h4>Premise</h4>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.<h4>Methods and results</h4>Target sequences used ...[more]
