Seawater carbonate chemistry and the amount of reads gained from small RNA sequencing of Anemonia viridis, supplement to: Urbarova, Ilona; Patel, Hardip; Forêt, S; Karlsen, Bard Ove; Jørgensen, Tor Erik; Hall-Spencer, Jason M; Johansen, Steinar D (2018): Elucidating the Small Regulatory RNA Repertoire of the Sea Anemone Anemonia viridis Based on Whole Genome and Small RNA Sequencing. Genome Biology and Evolution, 10(2), 410-426

• Main Authors: Urbarova, Ilona, Patel, Hardip, Forêt, S, Karlsen, Bard Ove, Jørgensen, Tor Erik, Hall-Spencer, Jason M, Johansen, Steinar D
• Format: Dataset
• Language: English
• Published: PANGAEA - Data Publisher for Earth & Environmental Science 2018
• Subjects: Anemonia viridis; Animalia; Benthic animals; Benthos; Cnidaria; CO2 vent; Coast and continental shelf; Field observation; Gene expression incl. proteomics; Mediterranean Sea; Single species; Temperate; Type; Species; Registration number of species; Uniform resource locator/link to reference; Identification; Reads; Percentage; Temperature, water; Temperature, water, standard deviation; Salinity; Salinity, standard deviation; pH; pH, standard deviation; Alkalinity, total; Partial pressure of carbon dioxide water at sea surface temperature wet air; Partial pressure of carbon dioxide, standard deviation; Carbon dioxide; Carbon dioxide, standard deviation; Carbon, inorganic, dissolved; Carbon, inorganic, dissolved, standard deviation; Bicarbonate ion; Bicarbonate ion, standard deviation; Carbonate system computation flag; Fugacity of carbon dioxide water at sea surface temperature wet air; Carbonate ion; Aragonite saturation state; Calcite saturation state; Calculated using CO2SYS; Calculated using seacarb after Nisumaa et al. 2010; Ocean Acidification International Coordination Centre OA-ICC; Johansen; Karlsen; Ocean acidification
• Online Access: https://dx.doi.org/10.1594/pangaea.892842; https://doi.pangaea.de/10.1594/PANGAEA.892842

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. : In order to allow full comparability with other ocean acidification data sets, the R package seacarb (Gattuso et al, 2016) was used to compute a complete and consistent set of carbonate system variables, as described by Nisumaa et al. (2010). In this dataset the original values were archived in addition with the recalculated parameters (see related PI). The date of carbonate chemistry calculation by seacarb is 2018-08-06.