Utilizing field collected insects for next generation sequencing: Effects of sampling, storage, and DNA extraction...

Area of Science:

• Genomics
• Molecular Biology
• Entomology

Background:

• Next-generation sequencing (NGS) enables genomic studies of non-model organisms.
• Many NGS protocols require high molecular weight DNA, difficult to obtain from field samples.
• DNA degradation in preserved specimens limits genomic research.

Purpose of the Study:

• Investigate the impact of insect capture and curation methods on ddRAD sequencing success.
• Evaluate DNA quality metrics for predicting sequencing outcomes.
• Compare DNA extraction methods for ddRAD library preparation.

Main Methods:

• Collected three wild bee species using five different methods.
• Performed Double-Digest Restriction Enzyme Associated DNA (ddRAD) sequencing on 105 specimens.
• Assessed DNA quality metrics and compared two extraction methods.

Main Results:

• All specimens yielded sufficient loci for population genetic analyses.
• Specimens preserved in 100% ethanol (net or trap-collected) produced higher quality ddRAD assemblies.
• Propylene glycol preservation resulted in lower quality assemblies.

Conclusions:

• Ethanol is recommended for preserving insect specimens for ddRAD sequencing.
• Rapid desiccation is key for high-quality DNA preservation.
• Diverse specimen types can be utilized for successful genomic analyses.