New targets acquired: Improving locus recovery from the Angiosperms353 probe set

Area of Science:

• Phylogenomics
• Molecular Evolution
• Bioinformatics

Background:

• Universal target enrichment kits are crucial for cost-effective phylogenetic studies across diverse taxa.
• The Angiosperms353 kit is widely used but its reference file has limited taxonomic representation, hindering read mapping and locus recovery.
• Insufficient sequence data in reference files can lead to reduced on-target reads and lower success rates in assembling target loci.

Purpose of the Study:

• To enhance the utility and cost-efficiency of universal target enrichment kits for broad evolutionary studies.
• To improve the mapping rate and recovery of target DNA sequences by expanding the reference file.
• To develop a more comprehensive reference dataset for the Angiosperms353 kit, increasing its effectiveness.

Main Methods:

• The Angiosperms353 target file was expanded by incorporating sequences from 566 additional transcriptomes, creating the 'mega353' target file.
• The mega353 file serves as a direct replacement for the original Angiosperms353 file within HybPiper analyses.
• Tools were developed for subsampling the mega353 file based on user-defined taxon groups and integrating other sequence data.

Main Results:

• The mega353 file resulted in an average 32% increase in on-target reads compared to the default Angiosperms353 file.
• Locus recovery at 75% length improved by 49% with the mega353 file.
• The total length of concatenated loci increased by 29% when using the expanded mega353 reference file.

Conclusions:

• Increasing the phylogenetic density of target reference files demonstrably improves the recovery of target capture loci.
• The enhanced mega353 file offers a significant improvement for DNA target enrichment in angiosperm research.
• The mega353 file and associated bioinformatics tools are publicly available to facilitate broader research applications.