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

Area of Science:

• Genomics
• Bioinformatics
• Evolutionary Biology

Background:

• Universal target enrichment probe kits are standard for phylogenetic studies but can be inefficient and costly.
• Identifying suitable marker loci for specific taxa can be challenging.

Purpose of the Study:

• To develop a computational pipeline for identifying a subset of promising candidate loci for phylogenetic studies.
• To provide a fast and cost-efficient method for marker mining.

Main Methods:

• A computational pipeline filters target sequences based on an assembled reference genome.
• The pipeline identifies intron-containing, single-copy loci present in the reference taxon.
• Demonstrated applicability using universal and family-specific probe kits with public reference genomes.

Main Results:

• LoCoLotive enables the identification of a subset of promising candidate loci.
• The approach was validated using two types of probe kits and multiple reference genomes.
• The accuracy of LoCoLotive is influenced by reference genome quality and relatedness.

Conclusions:

• LoCoLotive provides a fast and cost-efficient approach to marker mining, guided by commercial probe kits.
• This method is particularly useful when fewer marker loci are sufficient for phylogenetic analysis.
• The pipeline's effectiveness depends on the quality and evolutionary relatedness of the reference genome.