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A high-quality carabid genome provides insights into beetle genome evolution and cold adaptation
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  • Yi-Ming Weng,
  • Charlotte Francoeur,
  • Cameron Currie,
  • David Kavanaugh,
  • Sean Schoville
Yi-Ming Weng
University of Wisconsin Madison Graduate School
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Charlotte Francoeur
University of Wisconsin-Madison
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Cameron Currie
University of Wisconsin-Madison
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David Kavanaugh
California Academy of Sciences
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Sean Schoville
University of Wisconsin Madison
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Abstract

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.

Peer review status:ACCEPTED

23 Dec 2020Submitted to Molecular Ecology Resources
12 Jan 2021Submission Checks Completed
12 Jan 2021Assigned to Editor
19 Jan 2021Reviewer(s) Assigned
01 Mar 2021Review(s) Completed, Editorial Evaluation Pending
15 Mar 2021Editorial Decision: Revise Minor
13 Apr 2021Review(s) Completed, Editorial Evaluation Pending
13 Apr 20211st Revision Received
26 Apr 2021Editorial Decision: Accept