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Urbarova, Ilona; Patel, Hardip; Forêt, S; Karlsen, Bard Ove; Jørgensen, Tor Erik; Hall-Spencer, Jason M; Johansen, Steinar D (2018): Seawater carbonate chemistry and the amount of reads gained from small RNA sequencing of Anemonia viridis [dataset]. PANGAEA, https://doi.org/10.1594/PANGAEA.892842, Supplement to: Urbarova, I et al. (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

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Abstract:
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.
Keyword(s):
Anemonia viridis; Animalia; Benthic animals; Benthos; Cnidaria; CO2 vent; Coast and continental shelf; Field observation; Gene expression (incl. proteomics); Mediterranean Sea; Single species; Temperate
Further details:
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
Project(s):
Ocean Acidification International Coordination Centre (OA-ICC)
Comment:
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.
Parameter(s):
#NameShort NameUnitPrincipal InvestigatorMethod/DeviceComment
1 TypeTypeUrbarova, Ilonastudy
2 SpeciesSpeciesUrbarova, Ilona
3 Registration number of speciesReg spec noUrbarova, Ilona
4 Uniform resource locator/link to referenceURL refUrbarova, IlonaWoRMS Aphia ID
5 IdentificationIDUrbarova, IlonaIndividuals
6 ReadsReads#Urbarova, IlonaRaw reads
7 ReadsReads#Urbarova, IlonaFiltered Small RNA Reads (> or =18 nt)
8 PercentagePerc%Urbarova, Ilona% Reads Aligned to the Genome (> or =18 nt)
9 ReadsReads#Urbarova, IlonaFiltered Small RNA Reads (> or =23 nt)
10 PercentagePerc%Urbarova, Ilona% Reads Aligned to the Genome (> or = 23 nt)
11 ReadsReads#Urbarova, IlonaPutative piRNA Reads Aligned to Genomec
12 PercentagePerc%Urbarova, IlonaPutative piRNAs Aligned to Genome
13 Temperature, waterTemp°CUrbarova, Ilona
14 Temperature, water, standard deviationTemp std dev±Urbarova, Ilona
15 SalinitySalUrbarova, Ilona
16 Salinity, standard deviationSal std dev±Urbarova, Ilona
17 pHpHUrbarova, IlonaNBS scale
18 pH, standard deviationpH std dev±Urbarova, IlonaNBS scale
19 Alkalinity, totalATµmol/kgUrbarova, Ilona
20 Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)pCO2water_SST_wetµatmUrbarova, IlonaCalculated using CO2SYS
21 Partial pressure of carbon dioxide, standard deviationpCO2 std dev±Urbarova, IlonaCalculated using CO2SYS
22 Carbon dioxideCO2µmol/kgUrbarova, IlonaCalculated using CO2SYS
23 Carbon dioxide, standard deviationCO2 std dev±Urbarova, IlonaCalculated using CO2SYS
24 Carbon, inorganic, dissolvedDICµmol/kgUrbarova, IlonaCalculated using CO2SYS
25 Carbon, inorganic, dissolved, standard deviationDIC std dev±Urbarova, IlonaCalculated using CO2SYS
26 Bicarbonate ion[HCO3]-µmol/kgUrbarova, IlonaCalculated using CO2SYS
27 Bicarbonate ion, standard deviation[HCO3]- std dev±Urbarova, IlonaCalculated using CO2SYS
28 Carbonate system computation flagCSC flagYang, YanCalculated using seacarb after Nisumaa et al. (2010)
29 pHpHYang, YanCalculated using seacarb after Nisumaa et al. (2010)total scale
30 Carbon dioxideCO2µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
31 Fugacity of carbon dioxide (water) at sea surface temperature (wet air)fCO2water_SST_wetµatmYang, YanCalculated using seacarb after Nisumaa et al. (2010)
32 Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)pCO2water_SST_wetµatmYang, YanCalculated using seacarb after Nisumaa et al. (2010)
33 Bicarbonate ion[HCO3]-µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
34 Carbonate ion[CO3]2-µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
35 Carbon, inorganic, dissolvedDICµmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
36 Aragonite saturation stateOmega ArgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
37 Calcite saturation stateOmega CalYang, YanCalculated using seacarb after Nisumaa et al. (2010)
License:
Creative Commons Attribution 3.0 Unported (CC-BY-3.0)
Status:
Curation Level: Enhanced curation (CurationLevelC)
Size:
333 data points

Data

Download dataset as tab-delimited text — use the following character encoding:

1 
Type
(study)		2 
Species		3 
Reg spec no		4 
URL ref
(WoRMS Aphia ID)		5 
ID
(Individuals)		6 
Reads [#]
(Raw reads)		7 
Reads [#]
(Filtered Small RNA Reads (> o...)		8 
Perc [%]
(% Reads Aligned to the Genome...)		9 
Reads [#]
(Filtered Small RNA Reads (> o...)		10 
Perc [%]
(% Reads Aligned to the Genome...)		11 
Reads [#]
(Putative piRNA Reads Aligned ...)		12 
Perc [%]
(Putative piRNAs Aligned to Ge...)		13 
Temp [°C]		14 
Temp std dev [±]		15 
Sal		16 
Sal std dev [±]		17 
pH
(NBS scale)		18 
pH std dev [±]
(NBS scale)		19 
AT [µmol/kg]		20 
pCO2water_SST_wet [µatm]
(Calculated using CO2SYS)		21 
pCO2 std dev [±]
(Calculated using CO2SYS)		22 
CO2 [µmol/kg]
(Calculated using CO2SYS)		23 
CO2 std dev [±]
(Calculated using CO2SYS)		24 
DIC [µmol/kg]
(Calculated using CO2SYS)		25 
DIC std dev [±]
(Calculated using CO2SYS)		26 
[HCO3]- [µmol/kg]
(Calculated using CO2SYS)		27 
[HCO3]- std dev [±]
(Calculated using CO2SYS)		28 
CSC flag
(Calculated using seacarb afte...)		29 
pH
(total scale, Calculated using...)		30 
CO2 [µmol/kg]
(Calculated using seacarb afte...)		31 
fCO2water_SST_wet [µatm]
(Calculated using seacarb afte...)		32 
pCO2water_SST_wet [µatm]
(Calculated using seacarb afte...)		33 
[HCO3]- [µmol/kg]
(Calculated using seacarb afte...)		34 
[CO3]2- [µmol/kg]
(Calculated using seacarb afte...)		35 
DIC [µmol/kg]
(Calculated using seacarb afte...)		36 
Omega Arg
(Calculated using seacarb afte...)		37 
Omega Cal
(Calculated using seacarb afte...)
fieldAnemonia viridis (Cnidaria)856598marinespecies.orgpH 7.6-1161115171211793388.598317717681304.0664354986.519.100.438.130.057.710.302581181812015939233114710461267.59471441.441446237186.2225041.312.01
fieldAnemonia viridis (Cnidaria)856598marinespecies.orgpH 7.6-2124920901117576689.594655437721730.0679503288.019.100.438.130.057.710.302581181812015939233114710461267.59471441.441446237186.2225041.312.01
fieldAnemonia viridis (Cnidaria)856598marinespecies.orgpH 7.6-3137947611060987089.189211477238217.0631062487.219.100.438.130.057.710.302581181812015939233114710461267.59471441.441446237186.2225041.312.01
fieldAnemonia viridis (Cnidaria)856598marinespecies.orgpH 7.9-1188153441583761991.51323513111175365.01000143689.519.130.438.100.007.970.142607819286279222110716044267.8524750.257532245148.6524182.263.47
fieldAnemonia viridis (Cnidaria)856598marinespecies.orgpH 7.9-2200942531736979490.01624770413837596.01196059486.419.130.438.100.007.970.142607819286279222110716044267.8524750.257532245148.6524182.263.47
fieldAnemonia viridis (Cnidaria)856598marinespecies.orgpH 7.9-3167940891556704089.31495898512687556.01135393889.519.130.438.100.007.970.142607819286279222110716044267.8524750.257532245148.6524182.263.47
fieldAnemonia viridis (Cnidaria)856598marinespecies.orgpH 8.2-1130663191210975388.0113178339184500.0816361288.919.050.238.100.008.170.0625284376914219875322322268.0514423.744252012210.6022363.204.92
fieldAnemonia viridis (Cnidaria)856598marinespecies.orgpH 8.2-2173797051030915390.381241956661625.0554387083.219.050.238.100.008.170.0625284376914219875322322268.0514423.744252012210.6022363.204.92
fieldAnemonia viridis (Cnidaria)856598marinespecies.orgpH 8.2-3134923801122543690.387698657189261.0627132487.219.050.238.100.008.170.0625284376914219875322322268.0514423.744252012210.6022363.204.92