Towards large-scale museomics projects: a cost-effective and high-throughput extraction method for obtaining historical DNA from museum insect specimens

Abstract

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 to extracting genomic DNA from diverse insect specimens using single-phase reverse immobilization (SPRI) beads. We optimized PEG-8000 and NaCl concentrations to balance DNA yield and purity, reducing reagent cost to 6-11 cents per sample. 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 3,786 insect specimens across a broad range of ages, taxonomies, and tissue types. A detailed protocol is 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.