Seawater carbonate chemistry and the amount of reads gained from small RNA sequencing of Anemonia viridis
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 ane...
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ftpangaea:oai:pangaea.de:doi:10.1594/PANGAEA.892842 2023-05-15T17:52:09+02:00 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 2018-08-07 text/tab-separated-values, 333 data points https://doi.pangaea.de/10.1594/PANGAEA.892842 https://doi.org/10.1594/PANGAEA.892842 en eng PANGAEA Gattuso, Jean-Pierre; Epitalon, Jean-Marie; Lavigne, Héloïse; Orr, James C; Gentili, Bernard; Proye, Aurélien; Soetaert, Karline; Rae, James (2016): seacarb: seawater carbonate chemistry with R. R package version 3.1. https://cran.r-project.org/package=seacarb https://doi.pangaea.de/10.1594/PANGAEA.892842 https://doi.org/10.1594/PANGAEA.892842 CC-BY-3.0: Creative Commons Attribution 3.0 Unported Access constraints: unrestricted info:eu-repo/semantics/openAccess CC-BY 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, https://doi.org/10.1093/gbe/evy003 Alkalinity total Anemonia viridis Animalia Aragonite saturation state Benthic animals Benthos Bicarbonate ion standard deviation Calcite saturation state Calculated using CO2SYS Calculated using seacarb after Nisumaa et al. (2010) Carbon inorganic dissolved Carbonate ion Carbonate system computation flag Carbon dioxide 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 International Coordination Centre Partial pressure of carbon dioxide Partial pressure of carbon dioxide (water) at sea surface temperature (wet air) Percentage pH Reads Registration number of species Salinity Single species Species Temperate Dataset 2018 ftpangaea https://doi.org/10.1594/PANGAEA.892842 https://doi.org/10.1093/gbe/evy003 2023-01-20T09:11:22Z 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. Dataset Ocean acidification PANGAEA - Data Publisher for Earth & Environmental Science |
institution |
Open Polar |
collection |
PANGAEA - Data Publisher for Earth & Environmental Science |
op_collection_id |
ftpangaea |
language |
English |
topic |
Alkalinity total Anemonia viridis Animalia Aragonite saturation state Benthic animals Benthos Bicarbonate ion standard deviation Calcite saturation state Calculated using CO2SYS Calculated using seacarb after Nisumaa et al. (2010) Carbon inorganic dissolved Carbonate ion Carbonate system computation flag Carbon dioxide 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 International Coordination Centre Partial pressure of carbon dioxide Partial pressure of carbon dioxide (water) at sea surface temperature (wet air) Percentage pH Reads Registration number of species Salinity Single species Species Temperate |
spellingShingle |
Alkalinity total Anemonia viridis Animalia Aragonite saturation state Benthic animals Benthos Bicarbonate ion standard deviation Calcite saturation state Calculated using CO2SYS Calculated using seacarb after Nisumaa et al. (2010) Carbon inorganic dissolved Carbonate ion Carbonate system computation flag Carbon dioxide 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 International Coordination Centre Partial pressure of carbon dioxide Partial pressure of carbon dioxide (water) at sea surface temperature (wet air) Percentage pH Reads Registration number of species Salinity Single species Species Temperate Urbarova, Ilona Patel, Hardip Forêt, S Karlsen, Bard Ove Jørgensen, Tor Erik Hall-Spencer, Jason M Johansen, Steinar D Seawater carbonate chemistry and the amount of reads gained from small RNA sequencing of Anemonia viridis |
topic_facet |
Alkalinity total Anemonia viridis Animalia Aragonite saturation state Benthic animals Benthos Bicarbonate ion standard deviation Calcite saturation state Calculated using CO2SYS Calculated using seacarb after Nisumaa et al. (2010) Carbon inorganic dissolved Carbonate ion Carbonate system computation flag Carbon dioxide 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 International Coordination Centre Partial pressure of carbon dioxide Partial pressure of carbon dioxide (water) at sea surface temperature (wet air) Percentage pH Reads Registration number of species Salinity Single species Species Temperate |
description |
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 |
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 |
author_sort |
Urbarova, Ilona |
title |
Seawater carbonate chemistry and the amount of reads gained from small RNA sequencing of Anemonia viridis |
title_short |
Seawater carbonate chemistry and the amount of reads gained from small RNA sequencing of Anemonia viridis |
title_full |
Seawater carbonate chemistry and the amount of reads gained from small RNA sequencing of Anemonia viridis |
title_fullStr |
Seawater carbonate chemistry and the amount of reads gained from small RNA sequencing of Anemonia viridis |
title_full_unstemmed |
Seawater carbonate chemistry and the amount of reads gained from small RNA sequencing of Anemonia viridis |
title_sort |
seawater carbonate chemistry and the amount of reads gained from small rna sequencing of anemonia viridis |
publisher |
PANGAEA |
publishDate |
2018 |
url |
https://doi.pangaea.de/10.1594/PANGAEA.892842 https://doi.org/10.1594/PANGAEA.892842 |
genre |
Ocean acidification |
genre_facet |
Ocean acidification |
op_source |
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, https://doi.org/10.1093/gbe/evy003 |
op_relation |
Gattuso, Jean-Pierre; Epitalon, Jean-Marie; Lavigne, Héloïse; Orr, James C; Gentili, Bernard; Proye, Aurélien; Soetaert, Karline; Rae, James (2016): seacarb: seawater carbonate chemistry with R. R package version 3.1. https://cran.r-project.org/package=seacarb https://doi.pangaea.de/10.1594/PANGAEA.892842 https://doi.org/10.1594/PANGAEA.892842 |
op_rights |
CC-BY-3.0: Creative Commons Attribution 3.0 Unported Access constraints: unrestricted info:eu-repo/semantics/openAccess |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1594/PANGAEA.892842 https://doi.org/10.1093/gbe/evy003 |
_version_ |
1766159509243297792 |