Genome, transcriptome and methylome sequencing of a primitively eusocial wasp reveal a greatly reduced DNA methylation system in a social insect

Abstract

Comparative genomics of social insects has been intensely pursued in recent years with the goal of providing insights into the evolution of social behaviour and its underlying genomic and epigenomic basis. However, the comparative approach has been hampered by a paucity of data on some of the most informative social forms (e.g. incipiently and primitively social) and taxa (especially members of the wasp family Vespidae) for studying social evolution. Here, we provide a draft genome of the primitively eusocial model insect Polistes dominula, accompanied by analysis of casterelated transcriptome and methylome sequence data for adult queens and workers. Polistes dominula possesses a fairly typical hymenopteran genome, but shows very low genomewide GC content and some evidence of reduced genome size. We found numerous caste-related differences in gene expression, with evidence that both conserved and novel genes are related to caste differences. Most strikingly, these -omics data reveal a major reduction in one of the major epigenetic mechanisms that has been previously suggested to be important for caste differences in social insects: DNA methylation. Along with a conspicuous loss of a key gene associated with environmentally responsive DNA methylation (the de novo DNA methyltransferase Dnmt3), these wasps have greatly reduced genomewide methylation to almost zero. In addition to providing a valuable resource for comparative analysis of social insect evolution, our integrative -omics data for this important behavioural and evolutionary model system call into question the general importance of DNA methylation in caste differences and evolution in social insects.

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.…”

Transcriptomics of an extended phenotype: parasite manipulation of wasp social behaviour shifts expression of caste-related genes

“…Then, we created indexes for the reference genome in colour space and found candidate alignment locations (CALs). Next, local alignments were performed in CALs using the P. dominula reference genome [24] in nucleotide space. Finally, low-quality alignments were filtered by a post-processing step.…”

“…qRT-PCR was performed, using Power SYBR w Green PCR Master mix (Life Technologies), on the CFX384 Touch TM Real-Time PCR Detection System. Control genes were identified from the P. dominula genome [24], using best BLAST hits to control genes used in other studies and related taxa: these genes were homologous to other hymenopteran Actin and Elongation-factor 1a (EF1a) sequences. We also used an external control mCherry (Discosoma sp., [48]).…”

“…Third, X. vesparum have well-documented effects on their hosts, including behavioural and physiological changes that suggest they create 'wrong caste' phenotypes in hosts (described below) [18,19]. Fourth, P. dominula have new genomic data available, including a genome and caste-related transcriptome [18], and identified genes and pathways related to caste differences [24][25][26][27][28][29].…”

A novel post hoc method for detecting index switching finds no evidence for increased switching on the Illumina HiSeq X

“…Stinchcombe, 2017; Standage et al 2016;Li et al 2017). With the central role that sequencing 34 plays, it is alarming that a recent preprint suggests increased index switching on the new HiSeq 35 4000 and HiSeq X machines (Sinha et al 2017).…”