Introduction
Beetles (Coleoptera) are the most diverse animal group on the planet,
with more than 386,000 species described worldwide (Bouchard et
al. 2017; Forbes et al. 2018). The extremely high diversity and
abundance of beetles plays a critical role in most terrestrial
ecosystems (Brooks et al. 2012; Erwin 1997; Schowalter 2013;
Slade et al. 2019), with further significance to human society as
they serve as food, pests, pets, biological control agents, and models
in biological and engineering research (Adamski et al. 2019).
Despite their importance, relatively few genomic studies have been
conducted on beetles to date (McKenna 2018).
Coleoptera are divided into four suborders including Polyphaga,
Adephaga, Myxophaga, and Archostemata, based on both morphological and
molecular evidence (Beutel & Haas 2000; Zhang et al. 2018).
Among the four suborders, Polyphaga is the most diverse group,
comprising approximately 90% of coleopteran species, while most of the
remaining 10% comprise Adephaga (Grimaldi & Engel 2005). Carabidae is
the largest family of Adephaga, consisting of around 40,000 species, and
is known for its broad use of terrestrial habitats, ecosystem services,
and environmental sensitivity as bioindicators (Brooks et al.2012; Lorenz 2020). Except for a few species that are considered
agricultural pests (e.g. Zabrus tenebrioides ), most carabid
species are predators or scavengers that serve as beneficial biological
control agents and play key roles in local food webs (Georgescu et
al. 2017; Pizzolotto et al. 2018). Carabid beetles are found in
a wide range of habitats, spanning all terrestrial biomes, from tropical
and desert habitats, to arctic and alpine regions. As a result, they are
frequently used in studies of community ecology, conservation, and
biogeography (Kotze et al. 2011). Recent phylogenomic work has
provided an understanding of the evolutionary relationships of Carabidae
to other Coleoptera lineages and some patterns of gene family
diversification (Gustafson et al. 2019; McKenna et al.2019; Misof et al. 2014; Seppey et al. 2019a), but has not
provided a high-quality genome assembly for comparative analysis.
Carabid beetles are one of the few insect lineages that thrive in cold
habitats (Mani 1968). A strong positive relationship exists between
minimal environmental temperature and minimal temperature tolerance in
insects (Kimura 2004), because insects, as ectotherms, do not regulate
body heat through metabolism, but must instead physiologically adjust to
the surrounding environment (Addo‐Bediako et al. 2002). Cold
environments consequently pose a significant challenge to insects, with
few species surviving these conditions. Less than 2% of North American
insect species are found in the arctic biome (Danks et al. 2017),
and insect species richness declines dramatically in alpine and
sub-nival habitats (Nagy & Grabherr 2009). Carabid beetles, however,
are notable as arctic and alpine insects, comprising
~40-50% of beetle species richness in the arctic
(Chernov et al. 2000; Danks 1981), and setting the highest
altitudinal distribution record of Coleoptera, with three taxa
(Amara altiphila , Bembidion maddisoni , and Trechus
astrophilus ) reaching 5,600 m above sea level (a.s.l.) in the Himalayas
(Schmidt 2009; Schmidt et al. 2017). The carabid beetlePterostichus brevicornis additionally sets a record among beetles
in demonstrating extreme cold tolerance, where the LD50of overwintering adults occurs at -87°C (Baust 1972). The carabid genusNebria (> 500 species) is a notable example of a
cold-specialized beetle lineage, which exhibits its greatest diversity
and abundance at high latitude and high elevation (Lorenz 2020). For
example, 12 species of Nebria are found around Mount Rainier,
Washington, with four species inhabiting the alpine and sub-nival zone
(> 2000 m a.s.l., Kavanaugh 1985; Slatyer & Schoville
2016). Comparative genomic analysis of other insects has shown that
adaptation to cold environments might involve constraints in genome
architecture instead of gene content (Kelley et al. 2014; Kimet al. 2017), although other studies have mostly found evidence
of accelerated protein evolution (Cicconardi et al. 2020; Parkeret al. 2018). With the dual purpose of generating genomic
resources to investigate Carabid beetle genome evolution and cold
specialization, we assemble the genome of Nebria riversiVan Dyke (Carabidae: Nebriinae), an alpine ground beetle endemic to the
Sierra Nevada in California (2900–3910 m a.s.l.). Considering its
highly divergent taxonomic position from other Coleoptera genomes, and
as the only cold-specialized beetle genome sequenced to date, we
investigate genome architecture, gene family diversity, and differential
gene expression across life-stages and sexes. Finally, as the microbial
associates of high elevation insects have rarely been examined (Receveuret al. 2020), we scan genomic evidence for symbiotic microbes inN. riversi .