New targets

New targets improves locus recovery when using the Angiosperms353 probe set by expanding the Angiosperms353 target file into a comprehensive mega353 reference that increases taxonomic representation for target enrichment and read mapping.

Key Features:

• Expanded Taxonomic Representation: The mega353 target file incorporates sequences from 566 transcriptomes, increasing per-gene representation to 17–373 taxa compared to the original 6–18 taxa.
• Improved Mapping and Locus Recovery: Broadening the reference increases percentage of on-target reads by an average of 31%, increases locus recovery at 75% length by 61.9%, and expands total concatenated loci length by 30%.
• Flexibility and Customization: Supports subsampling the mega353 file by selected taxon groups and incorporation of additional transcriptome or protein-coding gene datasets.
• Integration with Existing Workflows: The mega353 file functions as a drop-in replacement for the original Angiosperms353 file in HybPiper analyses.

Scientific Applications:

• Angiosperm phylogenetics: Enables recovery of loci across broad angiosperm phylogenetic breadth to improve phylogenetic inference.
• Comparative genomics and assembly: Improved locus recovery and mapping accuracy produce more complete concatenated loci for studies of plant evolution and diversity.

Methodology:

Expands the Angiosperms353 target file by integrating sequences from 566 transcriptomes to enhance taxonomic representation and improve read mapping and locus recovery.