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| Main Authors: | , , , , , , |
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| Format: | Dataset Open Access |
| Language: | en |
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PANGAEA
2018
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| Online Access: | https://doi.org/10.1594/PANGAEA.892842 |
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| _version_ | 1867169129348202496 |
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| author | Urbarova, Ilona Patel, Hardip Forêt, S Karlsen, Bard Ove Jørgensen, Tor Erik Hall-Spencer, Jason M Johansen, Steinar D |
| author_facet | Urbarova, Ilona Patel, Hardip Forêt, S Karlsen, Bard Ove Jørgensen, Tor Erik Hall-Spencer, Jason M Johansen, Steinar D |
| collection | Datos científicos de ciencias marinas y ambientales |
| contents | 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. |
| format | Dataset Open Access |
| id | pangaea_https___doi_org_10_1594_PANGAEA_892842 |
| institution | PANGAEA |
| language | en |
| publishDate | 2018 |
| publisher | PANGAEA |
| record_format | pangaea |
| spellingShingle | Seawater carbonate chemistry and the amount of reads gained from small RNA sequencing of Anemonia viridis Urbarova, Ilona Patel, Hardip Forêt, S Karlsen, Bard Ove Jørgensen, Tor Erik Hall-Spencer, Jason M Johansen, Steinar D Alkalinity, total; Anemonia viridis; Animalia; Aragonite saturation state; Benthic animals; Benthos; Bicarbonate ion; Bicarbonate ion, standard deviation; Calcite saturation state; Calculated using CO2SYS; Calculated using seacarb after Nisumaa et al. (2010); Carbon, inorganic, dissolved; Carbon, inorganic, dissolved, standard deviation; Carbonate ion; Carbonate system computation flag; Carbon dioxide; Carbon dioxide, standard deviation; Cnidaria; CO2 vent; Coast and continental shelf; Field observation; Fugacity of carbon dioxide (water) at sea surface temperature (wet air); Gene expression (incl. proteomics); Identification; Mediterranean Sea; OA-ICC; Ocean acidification; Ocean Acidification International Coordination Centre; Partial pressure of carbon dioxide, standard deviation; Partial pressure of carbon dioxide (water) at sea surface temperature (wet air); Percentage; pH, NBS scale; pH, standard deviation; pH, total scale; Reads; Registration number of species; Salinity; Salinity, standard deviation; Single species; Species; Temperate; Temperature, water; Temperature, water, standard deviation; Type; Uniform resource locator/link to reference 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. |
| title | Seawater carbonate chemistry and the amount of reads gained from small RNA sequencing of Anemonia viridis |
| topic | Alkalinity, total; Anemonia viridis; Animalia; Aragonite saturation state; Benthic animals; Benthos; Bicarbonate ion; Bicarbonate ion, standard deviation; Calcite saturation state; Calculated using CO2SYS; Calculated using seacarb after Nisumaa et al. (2010); Carbon, inorganic, dissolved; Carbon, inorganic, dissolved, standard deviation; Carbonate ion; Carbonate system computation flag; Carbon dioxide; Carbon dioxide, standard deviation; Cnidaria; CO2 vent; Coast and continental shelf; Field observation; Fugacity of carbon dioxide (water) at sea surface temperature (wet air); Gene expression (incl. proteomics); Identification; Mediterranean Sea; OA-ICC; Ocean acidification; Ocean Acidification International Coordination Centre; Partial pressure of carbon dioxide, standard deviation; Partial pressure of carbon dioxide (water) at sea surface temperature (wet air); Percentage; pH, NBS scale; pH, standard deviation; pH, total scale; Reads; Registration number of species; Salinity; Salinity, standard deviation; Single species; Species; Temperate; Temperature, water; Temperature, water, standard deviation; Type; Uniform resource locator/link to reference |
| url | https://doi.org/10.1594/PANGAEA.892842 |