ABSTRACT
Ants are an emerging model system for neuroepigenetics, as embryos with very similar genomes develop into different adult castes that display strikingly different physiology, morphology, and behavior. Although a number of ant genomes have been sequenced to date, their draft quality is an obstacle to sophisticated analyses of epigenetic gene regulation. Using long reads generated with Pacific Biosystem single molecule real time sequencing, we have reassembled de novo high-quality genomes for the two ant species Camponotus floridanus and Harpegnathos saltator. The long reads allowed us to span large repetitive regions and join sequences previously in separate scaffolds, leading to a comprehensive and accurate protein-coding annotation that facilitated the identification of a Gp-9-like gene as differentially expressed in Harpegnathos castes. The new assemblies also enabled us to annotate long non-coding RNAs for the first time in ants, revealing several that were specifically expressed during Harpegnathos development and in the brains of different castes. These upgraded genomes, along with the new coding and non-coding annotations, will aid future efforts to shed light on the epigenetic mechanisms of phenotypic and behavioral plasticity in ants.