Elucidating the small regulatory RNA repertoire of the sea anemone Anemonia viridis based on whole genome and small RNA sequencing

• Published in: Genome Biology and Evolution
• Main Authors: Urbarova, Ilona, Patel, Hardip, Forêt, Sylvain, Karlsen, Bård Ove, Jørgensen, Tor Erik, Hall-Spencer, Jason M., Johansen, Steinar Daae
• Format: Article in Journal/Newspaper
• Language: English
• Published: Oxford University Press (OUP) 2018
• Subjects: VDP::Medisinske Fag: 700::Basale medisinske; odontologiske og veterinærmedisinske fag: 710::Medisinsk molekylærbiologi: 711; VDP::Medical disciplines: 700::Basic medical; dental and veterinary science disciplines: 710::Medical molecular biology: 711; coastal ecology; CO2 seep; ocean acidification; miRNA; piRNA; transposable elements; Ocean acidification
• Online Access: https://hdl.handle.net/10037/13253; https://doi.org/10.1093/gbe/evy003

Source at Genome Biology and Evolution https://doi.org/10.1093/gbe/evy003 . Accepted manuscript version, licensed CC BY-NC-ND 4.0. Cnidarians harbor a variety of small regulatory RNAs that include microRNAs (miRNAs) and PIWI-interacting RNAs (piRNAs), but detailed information is limited. Here, we report the identification and expression of novel miRNAs and putative piRNAs, as well as their genomic loci, in the symbiotic sea anemone Anemonia viridis . We generated a draft assembly of the A. viridis genome with putative size of 313 Mb that appeared to be composed of about 36% repeats, including known transposable elements. We detected approximately equal fractions of DNA transposons and retrotransposons. Deep sequencing of small RNA libraries constructed from A. viridis adults sampled at a natural CO2 gradient off Vulcano Island, Italy, identified 70 distinct miRNAs. Eight were homologous to previously reported miRNAs in cnidarians, whereas 62 appeared novel. Nine miRNAs were recognized as differentially expressed along the natural seawater pH gradient. We found a highly abundant and diverse population of piRNAs, with a substantial fraction showing ping–pong signatures. We identified nearly 22% putative piRNAs potentially targeting transposable elements within the A. viridis genome. The A. viridis genome appeared similar in size to that of other hexacorals with a very high divergence of transposable elements resembling that of the sea anemone genus Exaiptasia . The genome encodes and expresses a high number of small regulatory RNAs, which include novel miRNAs and piRNAs. Differentially expressed small RNAs along the seawater pH gradient indicated regulatory gene responses to environmental stressors.