Towards Large-Scale Museomics Projects: A Cost-Effective and High-Throughput Extraction Method for Obtaining...

Natural history collections serve as invaluable repositories of biodiversity data. Large-scale genomic analysis would greatly expand the utility and accessibility of museum collections, but the high cost and time-intensive nature of genomic methods limit such projects, particularly for invertebrate specimens. This paper presents an innovative, cost-effective and high-throughput approach for extracting genomic DNA from diverse insect specimens using single-phase reverse immobilisation (SPRI) beads. We optimised PEG-8000 and NaCl concentrations to balance DNA yield and purity, reducing reagent cost to 4.0-11.6¢ per sample, cost dependent on sample type. Our method was validated against three widely used extraction protocols and showed comparable DNA yield and amplification success to the widely used Qiagen DNeasy kit. We successfully applied the protocol in a high-throughput manner, extracting DNA from 3786 insect specimens across a broad range of ages, taxonomies and tissue types. A detailed protocol and instructional video are provided to facilitate the adoption of the method by other researchers. By improving one of the most crucial steps in any molecular project, this SPRI bead-based DNA extraction approach has significant potential for enabling large-scale museomics projects, thereby increasing the utility of historical collections for biodiversity research and conservation efforts.