High-quality long-read genome assemblies reveal evolutionary patterns of transposable elements and DNA methylation in termites

Abstract

SummaryTermites are social cockroaches that evolved eusociality independently from social Hymenoptera (ants, bees, wasps). Termites’ large genome sizes, generally composed of around 50% of transposable elements, make it challenging to obtain high quality genome assemblies with short-read sequencing technology. Correspondingly, there are only six published termite genome assemblies. Using PacBio HiFi sequencing, we generated high quality genome assemblies using single individuals for three additional termite species (Trinervitermessp.1,Odontotermessp.2,Macrotermes bellicosus) and a highly improved assembly for a fourth species (Cryptotermes secundus). We simultaneously profiled TE abundance and CpG DNA methylation from the same individuals. We show that TE abundance and DNA methylation levels across species reflect their phylogenetic relationships. We identified lineage- and species-specific TE- and DNA-methylation patterns, and revealed a negative correlation between TE abundance and methylation level. These results imply evolutionary arms-races between TE and DNA methylation during termite evolution.