bioRxiv Science⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/2024.09.11.612573

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

Holmquist, A. J.·Tavris, H.·Kim, G.·Esposito, L. A.·Fisher, B. L.·Lam, A.
View original source ↗Export metadata ↓

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.

Source connections

Explore related subjects

genomicsPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Holmquist, A. J., Tavris, H., Kim, G., Esposito, L. A., Fisher, B. L., Lam, A.. 2024-09-16. Towards large-scale museomics projects: a cost-effective and high-throughput extraction method for obtaining historical DNA from museum insect specimens. https://doi.org/10.1101/2024.09.11.612573

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Integrative Nanopore and Illumina sequencing reveals age-associated tRNA modification and CCA-tail dynamics in yeast

Aging is characterized by a progressive loss of proteostasis. Transfer RNAs (tRNAs) are essential regulators of translation, yet their dynamics during aging remain poorly understood due to challenges in sequencing highly modified RNAs. Here we present a benchmarked Nanopore direct RNA sequencing (RNA004 chemistry) resource that profiles the Saccharomyces cerevisiae tRNAome during replicative aging at single-molecule resolution. Using in vitro transcribed tRNA controls, we establish modification detection thresholds and validate key findings with orthogonal Illumina sequencing. While overall tRNA abundance remains largely stable, our resource reveals age-associated terminal A cleavage at the 3' CCA tail of mature tRNAs, targeted T-loop and anticodon modification changes, and single-molecule evidence of modification co-occurrence. This dataset provides a resource for exploring tRNA regulation, translation fidelity, and longevity.

genomics↗
bioRxiv2026

A hydrogen-producing mitochondrion in an anaerobic eukaryotrophic rhizarian

Diverse eukaryotes thrive under low oxygen conditions, in part through highly modified mitochondrion-related organelles (MROs) that use alternate metabolic pathways to support ATP production and cofactor recycling. Anaerobic lifestyles have evolved repeatedly across the eukaryotic tree of life, each providing an independent opportunity to understand how eukaryotes adapt to life in low oxygen conditions. Here, we use single-cell transcriptomics to reconstruct the MRO metabolism of PCE SSF, a benthic eukaryotrophic flagellate and the first cultivated representative of Novel Clade 12 (NC12; Rhizaria), an independently anaerobic rhizarian lineage. PCE SSF possesses an anaerobic hydrogen-producing mitochondrion capable of hydrogenosome-type substrate-level phosphorylation. It also retains a nearly complete but likely branched tricarboxylic acid pathway that lacks citrate synthase and malate dehydrogenase. The function of citrate synthase may instead be fulfilled by the typically cytosolic ATP citrate lyase, previously reported in this context only in the anaerobic cercozoan, Brevimastigomonas motovehiculus. Unlike B. motovehiculus, however, PCE SSF retains only Complex II and the NuoE/NuoF subunits of the electron transport chain and lacks a mitochondrial genome. Together, these features indicate an atypical and reduced mitochondrial metabolism, highlighting the diversity of evolutionary solutions to anaerobic energy metabolism in eukaryotes.

genomics↗
bioRxiv2026

Targeted CRISPRi screening reveals unexpected resilience across the RNA polymerase III transcriptome

Increased RNA polymerase III (Pol III) activity and tRNA abundance are widely linked to cancer cell growth, yet the functional requirement for individual Pol III genes and core components remains unclear, in part due to the difficulty of achieving gene-specific perturbation of highly conserved loci. Here, we developed an inducible CRISPR interference platform and a custom single-guide RNA (sgRNA) library enabling gene-specific targeting of Pol III-transcribed genes and Pol III machinery. Genome-wide screening identified several Pol III dependencies in diploid fibroblasts and HEK293T cells, including multiple initiator methionine tRNA genes among the strongest fitness dependencies. Unexpectedly, glioblastoma models remained largely insensitive to repression of both individual Pol III genes and core Pol III components, despite efficient target repression. These findings establish a general strategy for gene-specific interrogation of conserved Pol III genes and indicate that glioblastoma models tolerate extensive perturbation of Pol III genes and machinery.

genomics↗