DNA methylation is associated with codon degeneracy in a species of bumblebee

Abstract

Social insects display extreme phenotypic differences between sexes and castes even though the underlying genome can be almost identical. Epigenetic processes have been proposed as a possible mechanism for mediating these phenotypic differences. Using whole genome bisulfite sequencing of queens, males, and reproductive female workers we have characterised the sex- and caste-specific methylome of the bumblebee Bombus terrestris. We have identified a potential role for DNA methylation in histone modification processes which may influence sex and caste phenotypic differences. We also find differentially methylated genes generally show low levels of DNA methylation which may suggest a separate function for lowly methylated genes in mediating transcriptional plasticity, unlike highly methylated genes which are usually involved in housekeeping functions. We also examined the relationship between the underlying genome and the methylome using whole genome re-sequencing of the same queens and males. We find DNA methylation is enriched at zero-fold degenerate sites. We suggest DNA methylation may be acting as a targeted mutagen at these sites, providing substrate for selection via non-synonymous changes in the underlying genome. However, we did not see any relationship between DNA methylation and rates of positive selection in our samples. In order to fully assess a possible role for DNA methylation in adaptive processes a specifically designed study using natural population data is needed.

Constitutive and variable patterns of genome-wide DNA methylation in populations from spatial-environmental range extremes of the bumble beeBombus vosnesenskii

“…Heat shock protein machinery 89,90,91 and ion channel/transmembrane transport mechanisms 92 , especially those linked to calcium regulation 93 are widely recognized for their essential role in mediating molecular responses to thermal stress 93,94 , and have been previously observed in B. vosnesenskii 56,55 . The presence of chromatin-related GO terms in the top summarized GO term list is consistent with the potential involvement of CpG methylation in mediating access transcription machinery and particularly with a previously reported case of enrichment of chromatin related GO terms for differentially methylated genes related to caste determination in bumble bees 58 . Although the potential link between differential methylation and differential expression is still unclear in insects as there is mixed evidence if the differential methylation is positively correlated to differential expression 95,96 (but see 97,98,99,100,101 ) or differential exon usage 72,59 , these reported genes from our study could serve as promising candidates to more closely examine in future studies of thermal stress or other niche specific gene expression regulation in bumble bees.…”

“…The second objective of this study was to evaluate the potential for differences in methylation levels among B. vosnesenskii from the spatial-environmental extremes of its broad distribution. We identified 2,066 differentially methylated sites between the two populations and the genomic distribution of these differentially methylated CpGs matched the trends of general CpG methylation, and were similarly overrepresented in gene bodies, especially in exons, consistent with the distribution of differentially methylated sites between sexes and castes in the bumble bee B. terrestris 58 . The colder highelevation Oregon site exhibited lower percent methylation (1.03% ±0.04% SD) than warmer southern low-elevation sites in California (1.17% ± 0.06% SD), and 87.6% of differentially methylated sites were hypomethylated in the northern high-elevation samples.…”

“…Our first research objective was to characterize the constitutive methylome of B. vosnesenskii workers collected from diverse climatic regions within the species' range to identify features that were highly or rarely methylated in all individuals. The low genome-wide CpG methylation (~1.1%) is similar to other Hymenoptera 66 , including other bumble bees 59,60,58 , the honey bee Apis mellifera 67 , the wasp Nasonia vitripennis 68 . Such trends are generally common in holometabolous insects 31 apart from a few unusual instances 31 .…”

“…Several studies in arthropods indicate a potential role of gene body methylation in transcription elongation and alternative splicing 19 , based on the apparent correlation of CpG methylation with alternative splicing found in honeybees 67,75,30 and ants 69 . However, evidence from multiple insect orders suggests that CpG methylation is not directly correlated to differential exon usage 31,58,68 . The mixed evidence on the potential involvement of gene body methylation on alternative splicing indicates the need for future methylation studies in bumble bees that explore the possible link between CpG methylation and differential exon usage by utilizing complementary gene expression and methylation datasets.…”

“…The majority of epigenetics and DNA methylation studies in bumble bees have centered around determining its role in sex/caste determination 57,58 , reproduction 59 and development 60 using lab-reared individuals of two commonly used model species, B. terrestris, and B. impatiens 61 . However, little is known regarding the role of epigenetics in shaping niche-specific thermal adaptation in wild bumble bees, which might provide insights into the adaptive variation that could allow responses to environmental variation 62,63,2 .…”