The Genome and Methylome of a Beetle with Complex Social Behavior, Nicrophorus vespilloides (Coleoptera: Silphidae)

Abstract

Testing for conserved and novel mechanisms underlying phenotypic evolution requires a diversity of genomes available for comparison spanning multiple independent lineages. For example, complex social behavior in insects has been investigated primarily with eusocial lineages, nearly all of which are Hymenoptera. If conserved genomic influences on sociality do exist, we need data from a wider range of taxa that also vary in their levels of sociality. Here, we present the assembled and annotated genome of the subsocial beetle Nicrophorus vespilloides, a species long used to investigate evolutionary questions of complex social behavior. We used this genome to address two questions. First, do aspects of life history, such as using a carcass to breed, predict overlap in gene models more strongly than phylogeny? We found that the overlap in gene models was similar between N. vespilloides and all other insect groups regardless of life history. Second, like other insects with highly developed social behavior but unlike other beetles, does N. vespilloides have DNA methylation? We found strong evidence for an active DNA methylation system. The distribution of methylation was similar to other insects with exons having the most methylated CpGs. Methylation status appears highly conserved; 85% of the methylated genes in N. vespilloides are also methylated in the hymentopteran Nasonia vitripennis. The addition of this genome adds a coleopteran resource to answer questions about the evolution and mechanistic basis of sociality and to address questions about the potential role of methylation in social behavior.

Keywords: burying beetle; epigenetics; parental care; sociality.

Fig. 1.—

An adult female N. vespilloides regurgitating food into the mouth of her begging larvae on a prepared mouse carcass. Photograph by A. J. Moore.

Fig. 2.—

A two-ring pie chart showing results of annotation with BLAST against the complete UniProtKB database. First outer ring (gray) shows the proportion of gene models that could be annotated. Second ring (multicolored) shows the proportion of best BLAST hits of the annotations by order for all species with five or more best hits (97.8%). The best BLAST hits were overwhelmingly from other beetles and other Arthropods.

Fig. 3.—

Figure shows the results of the OrthoMCL analysis that clustered the proteomes of N. vespilloides, T. castaneum, A. mellifera, Na. vitripennis, D. melanogaster, and M. domestica into orthologous groupings. (A) A Venn diagram showing the overlap in the orthologous groupings of the two beetles (T. castaneum and N. vespilloides) and the two Hymenoptera (A. mellifera and Na. vitripennis). (B) A Venn diagram showing the overlap in orthologous groupings of the two beetles (T. castaneum and N. vespilloides) and the two Diptera (D. melanogaster and M. domestica).

Fig. 4.—

Summary of DNA methylation analyses. (A) A cladogram showing the relationship of the Dnmt’s across several insects and a mammal. Nves, N. vespilloides; Tcas, T. castaneum; Dmel, D. melanogaster; Cflo, C. floridanus; Amel, A. mellifera; Mmus, M. musculus; Znev, Zootermopsis nevadensis. (B) Number of methylated cytosines in each of the three replicates of N. vespilloides and T. castaneum. (C) A sequence logo of the overwhelming occurrence of methylation in CpG dinucleotide by showing the nucleotide proportions of the two nucleotides both upstream and downstream of the methylated cytosines. (D) A histogram of CpGs that are considered methylated versus the proportion of reads that supported their methylation status (weighted methylation level). (E) A density plot showing the very high symmetry of methylated CpG sites on opposing strands of DNA. (F) A pie chart showing the distribution of methylated CpGs across gene elements. (G) A standard box plot of the proportion of reads that supported methylation status (weighted methylation level) with genes grouped by whether they were methylated or not. (H) Diagram showing the proportion of reads that supported methylation (weighted methylation level) of methylated and unmethylated genes across each region of a gene model summarized as 20 bins within a region. (I) Histograms of methylated and unmethylated genes versus the CpG observed/expected ratio across a gene body. (J) Venn diagram illustrating the overlap of methylated genes that had 1:1 orthology between the burying beetle N. vespilloides and the jewel wasp Na. vitripennis.