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

• Published in: Cell reports (Cambridge) Vol. 23; no. 10; pp. 3078 - 3090
• Main Authors: Shields, Emily J., Sheng, Lihong, Weiner, Amber K., Garcia, Benjamin A., Bonasio, Roberto
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 05-06-2018
• Subjects: Animals; ants; Ants - genetics; Brain - metabolism; epigenetics; Gene Expression Regulation; Genes, Homeobox; Genome, Insect; genomes; Genomics - methods; long non-coding RNAs; Molecular Sequence Annotation; neuroepigenetics; Open Reading Frames - genetics; PacBio; RNA, Long Noncoding - genetics; RNA, Long Noncoding - metabolism; Sequence Analysis, RNA; social insects; ants; genomes; social insects; neuroepigenetics; long non-coding RNAs; epigenetics; PacBio
• ISSN: 2211-1247; 2211-1247
• DOI: 10.1016/j.celrep.2018.05.014

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.
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•Long reads produce highly contiguous genome assemblies for two ant species•Formerly unannotated gene well studied in other ants has caste-biased expression•Upgraded genomes allow for annotation of long non-coding RNAs•Many long non-coding RNAs are expressed in the brain, some in caste-specific manner
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.