The Genome and Methylome of a Subsocial Small Carpenter Bee,Ceratina calcarata

Abstract

Understanding the evolution of animal societies, considered to be a major transition in evolution, is a key topic in evolutionary biology. Recently, new gateways for understanding social evolution have opened up due to advances in genomics, allowing for unprecedented opportunities in studying social behavior on a molecular level. In particular, highly eusocial insect species (caste-containing societies with nonreproductives that care for siblings) have taken center stage in studies of the molecular evolution of sociality. Despite advances in genomic studies of both solitary and eusocial insects, we still lack genomic resources for early insect societies. To study the genetic basis of social traits requires comparison of genomes from a diversity of organisms ranging from solitary to complex social forms. Here we present the genome of a subsocial bee, Ceratina calcarata. This study begins to address the types of genomic changes associated with the earliest origins of simple sociality using the small carpenter bee. Genes associated with lipid transport and DNA recombination have undergone positive selection in C. calcarata relative to other bee lineages. Furthermore, we provide the first methylome of a noneusocial bee. Ceratina calcarata contains the complete enzymatic toolkit for DNA methylation. As in the honey bee and many other holometabolous insects, DNA methylation is targeted to exons. The addition of this genome allows for new lines of research into the genetic and epigenetic precursors to complex social behaviors.

Hemimetabolous genomes reveal molecular basis of termite eusociality

“…4b and Supplementary Table 16). These results show strong parallels to findings for eusocial Hymenoptera [40][41][42][43] . This is in stark contrast to the non-eusocial cockroach, B. germanica, where there was only a very weak relationship between CpG o/e and differential expression between nymphs and adult females (r = 0.14), nor were any large differences apparent in enriched GO terms between putatively methylated and non-methylated genes (Fig.…”

The effects of the neonicotinoid imidacloprid on gene expression and DNA methylation in the buff-tailed bumblebee Bombus terrestris

“…260 We found patterns of CpG methylation to be in line with other insect species. It is mainly 261 focused in exons (Glastad et al, 2017), and high CpG methylation was associated with highly 262 expressed genes (Figure 3) (Arsenault et al, 2018;Bonasio et al, 2012;Glastad et al, 2013;Libbrecht et al, 2016;Patalano et al, 2015;Wang et al, 2013), and non-differentially expressed 264 genes showed higher levels of methylation (Glastad et al, 2013(Glastad et al, , 2016Libbrecht et al, 2016;Sarda 265 et al, 2012). Neonicotinoids appear to have no effect on overall levels of CpG methylation (see wasp's (Nasonia) genome lacked non-CpG DNA methylation , and in this study, while we identified 270 a very small number of loci showing methylation in CHG/CHH contexts, we could not exclude the 271 possibility that much of it was noise, as bisulfite sequencing is prone to false positives from sources 272 such as incomplete bisulfite conversion, miscalled bases and SNPs.…”

Social behavior in bees influences the abundance ofSodalis(Enterobacteriaceae) symbionts

“…We therefore mined the Sodalis data from several previously collected genomic sequencing datasets, including 150 samples of the socially polymorphic Lasioglossum albipes and individual samples of 12 other halictid species. We also included all shotgun sequencing data collected for the five bee genomes sequenced in Kapheim et al (49) and Ceratina calcarata (50). We recovered large amounts of Sodalis data from 36 of the 150 L. albipes samples as well as six other halictids (H. ligatus, L. calceatum, L. leucozonium, L. malachurum, L. marginatum, and L. vierecki) and C. calcarata (Fig.…”

“…In addition, we made use of previously collected sequencing data for 13 other halictid species: Augochlorella aurata, Augochlora pura, Agapostemon virescens, Lasioglossum leucozonium, L. figueresi, L. marginatum, L. vierecki, L. zephyrum, L. calceatum, L. malachurum, L. oenotherae, L. pauxillum, and Halictus ligatus. Finally, to determine how widespread Sodalis is across bees, we also downloaded all raw data (excluding mate-pair libraries) sequenced as part of the 10 bee genome project (49) and for the Ceratina calcarata genome sequencing project (50). All raw datasets were filtered using the same methodology as the L. albipes dataset.…”