A high-quality carabid genome provides insights into beetle genome evolution and cold adaptation

The hyper-diverse order Coleoptera comprises a staggering ~25% of known
species on Earth. Despite recent breakthroughs in next generation
sequencing, there remains a limited representation of beetle diversity in
assembled genomes. Most notably, the ground beetle family Carabidae,
comprising more than 40,000 described species, has not been studied in a
comparative genomics framework using whole genome data. Here we generate a
high-quality genome assembly for Nebria riversi, to examine sources of
novelty in the genome evolution of beetles, as well as genetic changes
associated with specialization to high elevation alpine habitats. In
particular, this genome resource provides a foundation for expanding
comparative molecular research into mechanisms of insect cold adaptation.
Comparison to other beetles shows a strong signature of genome compaction,
with N. riversi possessing a relatively small genome (~147 Mb) compared to
other beetles, with associated reductions in repeat element content and
intron length. Small genome size is not, however, associated with fewer
protein-coding genes, and an analysis of gene family diversity shows
significant expansions of genes associated with cellular membranes and
membrane transport, as well as protein phosphorylation and muscle filament
structure. Finally, our genomic analyses show that these high elevation
beetles have endosymbiotic Spiroplasma, with several metabolic pathways
(e.g. propanoate biosynthesis) that might complement N. riversi, although
its role as a beneficial symbiont or as a reproductive parasite remains
equivocal.