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
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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Format: | Dataset |
Language: | English |
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PANGAEA - Data Publisher for Earth & Environmental Science
2018
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Online Access: | https://dx.doi.org/10.1594/pangaea.892842 https://doi.pangaea.de/10.1594/PANGAEA.892842 |
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ftdatacite:10.1594/pangaea.892842 |
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record_format |
openpolar |
institution |
Open Polar |
collection |
DataCite Metadata Store (German National Library of Science and Technology) |
op_collection_id |
ftdatacite |
language |
English |
topic |
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 |
spellingShingle |
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 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, 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 |
topic_facet |
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 |
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. : 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. |
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, 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 |
title_short |
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 |
title_full |
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 |
title_fullStr |
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 |
title_full_unstemmed |
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 |
title_sort |
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 |
publisher |
PANGAEA - Data Publisher for Earth & Environmental Science |
publishDate |
2018 |
url |
https://dx.doi.org/10.1594/pangaea.892842 https://doi.pangaea.de/10.1594/PANGAEA.892842 |
long_lat |
ENVELOPE(67.217,67.217,-70.544,-70.544) ENVELOPE(-46.000,-46.000,-60.350,-60.350) |
geographic |
Johansen Karlsen |
geographic_facet |
Johansen Karlsen |
genre |
Ocean acidification |
genre_facet |
Ocean acidification |
op_relation |
https://cran.r-project.org/package=seacarb https://dx.doi.org/10.1093/gbe/evy003 https://cran.r-project.org/package=seacarb |
op_rights |
Creative Commons Attribution 3.0 Unported https://creativecommons.org/licenses/by/3.0/legalcode cc-by-3.0 |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1594/pangaea.892842 https://doi.org/10.1093/gbe/evy003 |
_version_ |
1766158722203123712 |
spelling |
ftdatacite:10.1594/pangaea.892842 2023-05-15T17:51:32+02:00 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 Urbarova, Ilona Patel, Hardip Forêt, S Karlsen, Bard Ove Jørgensen, Tor Erik Hall-Spencer, Jason M Johansen, Steinar D 2018 text/tab-separated-values https://dx.doi.org/10.1594/pangaea.892842 https://doi.pangaea.de/10.1594/PANGAEA.892842 en eng PANGAEA - Data Publisher for Earth & Environmental Science https://cran.r-project.org/package=seacarb https://dx.doi.org/10.1093/gbe/evy003 https://cran.r-project.org/package=seacarb Creative Commons Attribution 3.0 Unported https://creativecommons.org/licenses/by/3.0/legalcode cc-by-3.0 CC-BY 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 Supplementary Dataset dataset Dataset 2018 ftdatacite https://doi.org/10.1594/pangaea.892842 https://doi.org/10.1093/gbe/evy003 2021-11-05T12:55:41Z 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. Dataset Ocean acidification DataCite Metadata Store (German National Library of Science and Technology) Johansen ENVELOPE(67.217,67.217,-70.544,-70.544) Karlsen ENVELOPE(-46.000,-46.000,-60.350,-60.350) |