Sequence capture using PCR-generated probes: a cost-effective method of targeted high-throughput sequencing for...

Area of Science:

• Genomics
• Evolutionary Biology
• Molecular Biology

Background:

• High-throughput sequencing and subgenomic enrichment advance population genetics and phylogenetics.
• Targeted genome enrichment is crucial for studying nonmodel organisms.

Purpose of the Study:

• To modify the sequence capture using PCR-generated probes (SCPP) protocol for improved efficiency and broader applicability.
• To enable cost-effective, targeted enrichment of specific genomic regions for population and phylogenetic studies.

Main Methods:

• Modification of an existing in-solution capture protocol using PCR products as target probes.
• Multiplexing indexed samples for sequencing predominantly orthologous, targeted genomic regions.
• Application of the Sequence Capture using PCR-generated Probes (SCPP) protocol without specialized equipment.

Main Results:

• Achieved higher capture efficiencies and locus coverage across a wider phylogenetic range of taxa.
• Demonstrated efficient and consistent capture in multiple SCPP experiments at various phylogenetic distances.
• Reduced experimental costs for projects requiring a modest scale of genetic data (25-100 loci).

Conclusions:

• The modified SCPP protocol is a flexible, cost-effective tool for population genetics and phylogenetics.
• This method enhances the study of nonmodel organisms, extending its utility to phylogeographic and phylogenomic research.
• The protocol's efficiency and consistency support its application in diverse evolutionary studies.