Gustafson, G. | Search bioRxiv

bioRxiv2026

Three annotated tiger beetle genomes (Coleoptera, Adephaga, Cicindelidae)

Advances and accessibility to next-generation technology provide opportunities to sequence non-model organisms. Despite this increase in whole-genome sequencing data, annotation and the production of reference genomes remain limited. Reference genomes are a critical tool for a variety of studies in evolutionary biology, functional genomics, and conservation genetics. Tiger beetles (Cicindelidae) are a diverse and globally distributed family of beetles that serve as bioindicator taxa and flagship species for insect conservation. Here, we report highly complete, contiguous, and annotated genome assemblies representing draft reference genomes for three species of tiger beetle spanning the phylogeny. These draft reference genomes are for Audouins night-stalking tiger beetle, Omus audouini; the montane giant tiger beetle, Amblycheila baroni; and the western red-bellied tiger beetle, Cicindelidia sedecimpunctata. Article SummaryTiger beetles are a charismatic group with [~]3000 species distributed globally. Despite their popularity among insect enthusiasts and their role as bioindicators of ecosystem health, the group currently lacks a reference genome. This article outlines genome assembly and annotation for three tiger beetle species that span evolutionary relationships within the lineage. Quality control analyses show that the assemblies are reference quality and demonstrate high contiguity, completeness, and accuracy. The resulting draft genome annotations will be a valuable resource for scientific endeavors and allow for continued research on tiger beetles and their allies.

genomics↗

bioRxiv2023

To design or not to design? Comparison of beetle ultraconserved element probe set utility based on phylogenetic distance, breadth, and method of probe design

Tailoring ultraconserved element (UCE) probe set design to focal taxa has been demonstrated to improve locus recovery and phylogenomic inference. However, beyond conducting expensive in vitro testing, it remains unclear how best to determine whether an existing UCE probe set is likely to suffice for phylogenomic inference, or if tailored probe design will be desirable. Here we investigate the utility of eight different UCE probe sets for the in silico phylogenomic inference of scarabaeoid beetles. Probe sets tested differed in terms of (1) how phylogenetically distant from Scarabaeoidea taxa those used during probe design are, (2) breadth of phylogenetic inference probe set was designed for, and (3) method of probe design. As part of this study, two new UCE probe sets are produced for the beetle family Scarabaeidae and superfamily Hydrophiloidea. We find that, predictably, probe set utility decreases with increasing phylogenetic distance of design taxa from focal taxa, as well as with narrower breadth of phylogenetic inference probes were designed for. We also confirm previous findings regarding ways to optimize UCE probe design. Finally, we make suggestions regarding assessment of need for de novo probe design and reinforce previous proposed methods for maximizing UCE probe design to improve phylogenomic inference.

evolutionary biology↗