Liew, Yi Jin; Zoccola, Didier; Li, Yong; Tambutté, Eric; Venn, Alexander A; Michell, Craig T; Cui, Guoxin; Deutekom, Eva S; Kaandorp, Jaap A; Voolstra, Christian R; Forêt, S; Allemand, Denis; Tambutté, Sylvie; Aranda, Manuel (2023): Seawater carbonate chemistry and cell growth of coral Stylophora pistillata [dataset]. PANGAEA, https://doi.org/10.1594/PANGAEA.959452
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Abstract:
There are increasing concerns that the current rate of climate change might outpace the ability of reef-building corals to adapt to future conditions. Work on model systems has shown that environmentally induced alterations in DNA methylation can lead to phenotypic acclimatization. While DNA methylation has been reported in corals and is thought to associate with phenotypic plasticity, potential mechanisms linked to changes in whole-genome methylation have yet to be elucidated. We show that DNA methylation significantly reduces spurious transcription in the coral Stylophora pistillata. Furthermore, we find that DNA methylation also reduces transcriptional noise by fine-tuning the expression of highly expressed genes. Analysis of DNA methylation patterns of corals subjected to long-term pH stress showed widespread changes in pathways regulating cell cycle and body size. Correspondingly, we found significant increases in cell and polyp sizes that resulted in more porous skeletons, supporting the hypothesis that linear extension rates are maintained under conditions of reduced calcification. These findings suggest an epigenetic component in phenotypic acclimatization that provides corals with an additional mechanism to cope with environmental change.
Keyword(s):
Supplement to:
Liew, Yi Jin; Zoccola, Didier; Li, Yong; Tambutté, Eric; Venn, Alexander A; Michell, Craig T; Cui, Guoxin; Deutekom, Eva S; Kaandorp, Jaap A; Voolstra, Christian R; Forêt, S; Allemand, Denis; Tambutté, Sylvie; Aranda, Manuel (2018): Epigenome-associated phenotypic acclimatization to ocean acidification in a reef-building coral. Science Advances, 4(6), eaar8028, https://doi.org/10.1126/sciadv.aar8028
Documentation:
Gattuso, Jean-Pierre; Epitalon, Jean-Marie; Lavigne, Héloïse; Orr, James; Gentili, Bernard; Hagens, Mathilde; Hofmann, Andreas; Mueller, Jens-Daniel; Proye, Aurélien; Rae, James; Soetaert, Karline (2022): seacarb: seawater carbonate chemistry with R. R package version 3.3.1. https://cran.r-project.org/web/packages/seacarb/index.html
Project(s):
Comment:
In order to allow full comparability with other ocean acidification data sets, the R package seacarb (Gattuso et al, 2022) 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 2023-05-23.
Parameter(s):
License:
Creative Commons Attribution 4.0 International (CC-BY-4.0)
Status:
Curation Level: Enhanced curation (CurationLevelC)
Size:
68 data points
Data
| 1 Study type | 2 Species UID | 3 Species UID (URI) | 4 Species UID (Semantic URI) | 5 Treat | 6 Cell size [µm] | 7 Cell size std e [±] | 8 Calyx size [mm] | 9 Calyx size std e [±] | 10 Skel poros [%] | 11 Skel poros std e [±] | 12 Sal | 13 Temp [°C] | 14 pH (total scale, Spectrophotometric) | 15 pH std dev [±] (total scale, Spectrophotometric) | 16 AT [µmol/kg] (Potentiometric titration) | 17 AT std dev [±] (Potentiometric titration) | 18 pCO2water_SST_wet [µatm] (Calculated using CO2SYS) | 19 pCO2 std dev [±] (Calculated using CO2SYS) | 20 [HCO3]- [µmol/kg] (Calculated using CO2SYS) | 21 [HCO3]- std dev [±] (Calculated using CO2SYS) | 22 [CO3]2- [µmol/kg] (Calculated using CO2SYS) | 23 [CO3]2- std dev [±] (Calculated using CO2SYS) | 24 DIC [µmol/kg] (Calculated using CO2SYS) | 25 DIC std dev [±] (Calculated using CO2SYS) | 26 Omega Arg (Calculated using CO2SYS) | 27 Omega Arg std dev [±] (Calculated using CO2SYS) | 28 CSC flag (Calculated using seacarb afte...) | 29 CO2 [µmol/kg] (Calculated using seacarb afte...) | 30 fCO2water_SST_wet [µatm] (Calculated using seacarb afte...) | 31 pCO2water_SST_wet [µatm] (Calculated using seacarb afte...) | 32 [HCO3]- [µmol/kg] (Calculated using seacarb afte...) | 33 [CO3]2- [µmol/kg] (Calculated using seacarb afte...) | 34 DIC [µmol/kg] (Calculated using seacarb afte...) | 35 Omega Arg (Calculated using seacarb afte...) | 36 Omega Cal (Calculated using seacarb afte...) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| laboratory | Stylophora pistillata | marinespecies.org | urn:lsid:marinespecies.org:taxname:206982 | pH 7.2 | 5.3 | 0.038747236 | 1.191 | 0.025 | 72.25 | 0.192 | 38 | 25 | 7.22 | 0.01 | 2496.62 | 6.99 | 3513.15 | 67.20 | 2384.13 | 4.42 | 46.25 | 1.08 | 2528.27 | 3.62 | 0.72 | 0.02 | 8 | 98.92 | 3538.74 | 3550.11 | 2385.34 | 45.76 | 2530.01 | 0.71 | 1.07 |
| laboratory | Stylophora pistillata | marinespecies.org | urn:lsid:marinespecies.org:taxname:206982 | pH 8.0 | 5.2 | 0.037786347 | 1.030 | 0.030 | 62.48 | 2.491 | 38 | 25 | 7.95 | 0.00 | 2447.48 | 7.16 | 537.66 | 4.88 | 1951.14 | 1.90 | 202.41 | 2.25 | 2168.53 | 4.02 | 3.14 | 0.03 | 8 | 15.09 | 539.74 | 541.47 | 1953.82 | 201.28 | 2170.18 | 3.12 | 4.72 |