High-Quality Genome Assemblies Reveal Long Non-coding RNAs Expressed in Ant Brains

Emily J. Shields, Lihong Sheng, Amber K. Weiner, Benjamin A. Garcia, Roberto Bonasio

Research output: Contribution to journalArticlepeer-review

37 Scopus citations


Ants are an emerging model system for neuroepigenetics, as embryos with virtually identical genomes develop into different adult castes that display diverse 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. We reassembled de novo high-quality genomes for two ant species, Camponotus floridanus and Harpegnathos saltator. Using long reads enabled us to span large repetitive regions and improve genome contiguity, leading to comprehensive and accurate protein-coding annotations 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 in ants, revealing caste-, brain-, and developmental-stage-specific long non-coding RNAs (lncRNAs) in Harpegnathos. These upgraded genomes, along with the new gene annotations, will aid future efforts to identify epigenetic mechanisms of phenotypic and behavioral plasticity in ants. Using long-read sequencing, Shields et al. upgrade the genome assemblies for two ant species. Their results reveal a protein-coding gene preferentially expressed in worker ants and genes for long non-coding RNAs, several of which were expressed in the brain, in some cases at different levels in workers and reproductives.

Original languageEnglish
Pages (from-to)3078-3090
Number of pages13
JournalCell Reports
Issue number10
StatePublished - Jun 5 2018


  • PacBio
  • ants
  • epigenetics
  • genomes
  • long non-coding RNAs
  • neuroepigenetics
  • social insects


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