Reference genome of the bicolored carpenter ant, Camponotus vicinus

Abstract

Carpenter ants in the genus Camponotus are large, conspicuous ants that are abundant and ecologically influential in many terrestrial ecosystems. The bicolored carpenter ant, Camponotus vicinus Mayr, is distributed across a wide range of elevations and latitudes in western North America, where it is a prominent scavenger and predator. Here, we present a high-quality genome assembly of C. vicinus from a sample collected in Sonoma County, California, near the type locality of the species. This genome assembly consists of 38 scaffolds spanning 302.74 Mb, with contig N50 of 15.9 Mb, scaffold N50 of 19.9 Mb, and BUSCO completeness of 99.2%. This genome sequence will be a valuable resource for exploring the evolutionary ecology of C. vicinus and carpenter ants generally. It also provides an important tool for clarifying cryptic diversity within the C. vicinus species complex, a genetically diverse set of populations, some of which are quite localized and of conservation interest.

Keywords: Blochmannia; California Conservation Genomics Project; Camponotini; Formicidae; endosymbiont.

Fig. 1.

Bicolored carpenter ant reference genome assembly. A) A major worker of the bicolored carpenter ant, Camponotus vicinus (photo: Elizabeth Cash). B) Phylogenetic reconstruction based on whole genome sequences of C. vicinus (California, this study) compared with nine other Camponotus species from Shields et al. (2018), Manthey et al. (2022), and Faulk (2023). Filled circles represent 100% bootstrap support. Sample names from Manthey et al. (2022) are shown in parentheses. C) Scatterplot comparing C. vicinus genome assembly (red) to assemblies of C. floridanus (yellow = 2016 assembly, Shield et al. 2018; blue = 2010 assembly Bonasio et al. 2010), C. pennsylvanicus (green, Faulk 2023), and other non-Camponotus ant species (black = long-read sequencing, gray = short-read sequencing; n = 80 total assemblies representing 59 species) based on the natural log (ln) of contig number and contig N50 values. D) Lineplot comparing scaffold/contig sizes (Mb) and cumulative genome coverage (%) for C. vicinus (red, scaffolds), C. floridanus (2016, yellow, scaffolds), and C. pennsylvanicus (green, contigs) genome assemblies along with four representative ant genomes with chromosome-level assemblies (Cataglyphis hispanica [gray, dashed], Monomorium pharonsis [black, solid], Ooceraea biroi [black, dashed], and Solenopsis invicta [gray, solid]).

Fig. 2.

Visual overview of genome assembly metrics. A) K-mer spectra output generated from PacBio HiFi data without adapters using GenomeScope2.0. The unimodal pattern observed corresponds to a haploid genome. B) Omni-C Contact map for the genome assembly generated with PretextSnapshot. The Omni-C contact map translates proximity of genomic regions in 3-D space to contiguous linear organization. Each cell in the contact map corresponds to sequencing data supporting the linkage (or join) between two of such regions. Scaffolds are separated by black lines and higher density corresponds to higher levels of fragmentation. C) BlobToolKit Snail plot showing a graphical representation of the quality metrics presented in Table 3 for the C. vicinus primary assembly. The plot circle represents the full size of the assembly. From the inside to the outside, the central plot covers length-related metrics. The red line represents the size of the longest scaffold; all other scaffolds are arranged in size order moving clockwise around the plot and drawn in gray starting from the outside of the central plot. Dark and light orange arcs show the scaffold N50 and scaffold N90 values. The central light gray spiral shows the cumulative scaffold count with a white line at each order of magnitude. White regions in this area reflect the proportion of Ns in the assembly. The dark vs. light blue area around it shows mean, maximum and minimum GC vs. AT content at 0.1% intervals.