Caste-Specific RNA Editomes And Comparative Analyses In The Leaf-Cutting Ant

In eusociality, an evolutionarily advanced level of colonial existence, adult colonial members belong to two or more overlapping generations, care cooperatively for the young, and are divided into reproductive and nonreproductive castes. Eusocial insects have evolved the capacity to generate adults with distinct morphological, reproductive and behavioural phenotypes from the same genome.Recently, epigenetic mechanisms have been proposed to have key regulatory roles in eusocial polyphenisms. RNA editing is a post-transcriptional-processing mechanism, which alters RNA sequences by insertion/deletion or modification of specific nucleotides resulted in the information in the mature RNA differs from that defined in the genome. Recent studies suggest that RNA editing might enhance the diversity of gene products at the post-transcriptional level, particularly to induce functional changes in the nervous system. RNA editing in nervous systems of eusocial insects could therefore be a potential regulatory mechanism for caste differentiation and division of labor.Here we develop a flexible and efficient software package to facilitate the study of RNA editing, and use strand-specific RNA-Seq on head tissue samples of the female castes of Acromyrmex echinatior and data from other genome-sequenced ants to evaluate the possible role of RNA editing in modulating functional gene differentiation among castes. Our main conclusions are listed as follows:1. Compared with previous studies, the advantage of our software is that it introduces rigorous statistic analyses based on Bayesian model to estimate the genomic homozygosity from DNA-Seq data for the candidate editing sites. Our software also implements a statistic model based on Binomial distribution and multiple stringent filters to remove false positives from sequencing or read-mapping errors. Furthermore, with the statistic models mentioned above, our software is capable of handling both samples from an individual and a pool of multiple individuals.2. We report the first comprehensive investigation of RNA editomes in a eusocial insect, the leaf-cutting ant A. echinatior. The large majority of RNA editing changes were A-to-I editing, and the characteristics of A. echinatior A-to-I editing sites were generally similar to what has been found in humans, mice and fruit flies, indicating that the function of ADAR(adenosine deaminase acting on RNA) enzymes is highly conserved.3. Using head samples from the leaf-cutting ant A. echinatior, we compare RNA editomes across eusocial castes, identifying ca. 11,000 RNA editing sites in gynes, large workers and small workers. Those editing sites map to 800 genes functionally enriched for neurotransmission, circadian rhythm, temperature response, RNA splicing and carboxylic acid biosynthesis.4. Most A. echinatior editing sites are species-specific, but 8–23% of them are conserved across ant subfamilies and likely to have been important for the evolution of eusociality in ants.5. The level of editing varies for the same site between castes, suggesting that RNA editing might be a general mechanism that shapes caste behaviour in ants.Overall, our results imply that caste differentiation in ants and possibly other eusocial insects is likely to be affected by RNA editing and that this mechanism may represent a novel and general mechanism for shaping caste morphology and behavior via plastic gene expression in nervous systems.