Draft genome of the endemic alpine ground beetle Carabus (Platycarabus) depressus (Coleoptera: Carabidae) from long-read sequencing of a frozen archived specimen.

Abstract

The rapid advancement of genomic technologies has enabled the production of highly contiguous reference genomes for non-model organisms. However, these methods often require exceptionally fresh material containing unfragmented high molecular weight nucleic acids. Researchers who preserve field-collected specimens in ethanol at ambient temperatures, prior to transferring them to long-term frozen archives, face challenges in applying advanced genomic approaches due to DNA and RNA fragmentation under suboptimal preservation conditions. To explore the potential of such preserved specimens as sources of reference genomes, we utilized Nanopore MinION technology to generate genomic data from a frozen archived specimen of the endemic alpine ground beetle Carabus (Platycarabus) depressus. Using a rapid in-house protocol for high molecular weight DNA extraction, followed by sequencing on a single flow cell, we produced 8.75 million raw reads with an N50 of 2.8 Kb. The resulting assembly achieved remarkable completeness, recovering up to 98% of BUSCO genes, despite a moderate N50 of 945 Kb. This genome is only the second available for the taxonomically diverse genus Carabus and highlights the feasibility of performing short-to-long-read sequencing from frozen archived specimens commonly housed in natural history collections. These findings open new avenues for advancing non-model organism genomics and its downstream applications.