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de Wit, Pierre; Durland, Evan; Ventura, Alexander; Langdon, Chris (2018): Seawater carbonate chemistry and gene expression, shell formation in larval Pacific oysters (Crassostrea gigas) [dataset]. PANGAEA, https://doi.org/10.1594/PANGAEA.893428, Supplement to: de Wit, P et al. (2018): Gene expression correlated with delay in shell formation in larval Pacific oysters (Crassostrea gigas) exposed to experimental ocean acidification provides insights into shell formation mechanisms. BMC Genomics, 19(1), https://doi.org/10.1186/s12864-018-4519-y

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Abstract:
Background: Despite recent work to characterize gene expression changes associated with larval development in oysters, the mechanism by which the larval shell is first formed is still largely unknown. In Crassostrea gigas, this shell forms within the first 24 h post fertilization, and it has been demonstrated that changes in water chemistry can cause delays in shell formation, shell deformations and higher mortality rates. In this study, we use the delay in shell formation associated with exposure to CO2-acidified seawater to identify genes correlated with initial shell deposition.
Results: By fitting linear models to gene expression data in ambient and low aragonite saturation treatments, we are able to isolate 37 annotated genes correlated with initial larval shell formation, which can be categorized into 1) ion transporters, 2) shell matrix proteins and 3) protease inhibitors. Clustering of the gene expression data into co-expression networks further supports the result of the linear models, and also implies an important role of dynein motor proteins as transporters of cellular components during the initial shell formation process.
Conclusions: Using an RNA-Seq approach with high temporal resolution allows us to identify a conceptual model for how oyster larval calcification is initiated. This work provides a foundation for further studies on how genetic variation in these identified genes could affect fitness of oyster populations subjected to future environmental changes, such as ocean acidification.
Keyword(s):
Animalia; Bottles or small containers/Aquaria (<20 L); Calcification/Dissolution; Coast and continental shelf; Crassostrea gigas; Gene expression (incl. proteomics); Laboratory experiment; Mollusca; North Pacific; Pelagos; Single species; Temperate; Zooplankton
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
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 2018-09-04.
Parameter(s):
#NameShort NameUnitPrincipal InvestigatorMethod/DeviceComment
TypeTypede Wit, Pierrestudy
SpeciesSpeciesde Wit, Pierre
Registration number of speciesReg spec node Wit, Pierre
Uniform resource locator/link to referenceURL refde Wit, PierreWoRMS Aphia ID
ExperimentExpde Wit, Pierre
TreatmentTreatde Wit, Pierre
Time in hoursTimehde Wit, Pierretime post fertilization
IndividualsInd#de Wit, Pierrecount, replicate 1
IndividualsInd#de Wit, Pierrepartially calcified, replicate 1
10 IndividualsInd#de Wit, Pierrefully calcified, replicate 1
11 IndividualsInd#de Wit, Pierrecount, replicate 2
12 IndividualsInd#de Wit, Pierrepartially calcified, replicate 2
13 IndividualsInd#de Wit, Pierrefully calcified, replicate 2
14 Calcification indexCalc Ide Wit, Pierre
15 Calcification index, standard deviationCalc I std dev±de Wit, Pierre
16 mRNA gene expression, relativemRNA expressde Wit, Pierre
17 mRNA gene expression, relative, standard deviationmRNA express std dev±de Wit, Pierre
18 mRNA gene expression, relative, standard errormRNA express std e±de Wit, Pierre
19 mRNA gene expression, relativemRNA expressde Wit, PierreTyrosinase (contig CGI_10007793) expression
20 Temperature, waterTemp°Cde Wit, Pierre
21 Temperature, water, standard deviationTemp std dev±de Wit, Pierre
22 SalinitySalde Wit, Pierre
23 Salinity, standard deviationSal std dev±de Wit, Pierre
24 Alkalinity, totalATµmol/kgde Wit, Pierre
25 Alkalinity, total, standard deviationAT std dev±de Wit, Pierre
26 Carbon, inorganic, dissolvedDICµmol/kgde Wit, Pierre
27 Carbon, inorganic, dissolved, standard deviationDIC std dev±de Wit, Pierre
28 Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)pCO2water_SST_wetµatmde Wit, Pierre
29 Partial pressure of carbon dioxide, standard deviationpCO2 std dev±de Wit, Pierre
30 Carbon, inorganic, dissolvedDICµmol/kgde Wit, Pierre
31 Carbon, inorganic, dissolved, standard deviationDIC std dev±de Wit, Pierre
32 Bicarbonate ion[HCO3]-µmol/kgde Wit, Pierre
33 Bicarbonate ion, standard deviation[HCO3]- std dev±de Wit, Pierre
34 pHpHde Wit, Pierretotal scale
35 pH, standard deviationpH std dev±de Wit, Pierretotal scale
36 Aragonite saturation stateOmega Argde Wit, Pierre
37 Aragonite saturation state, standard deviationOmega Arg std dev±de Wit, Pierre
38 Carbonate system computation flagCSC flagYang, YanCalculated using seacarb after Nisumaa et al. (2010)
39 pHpHYang, YanCalculated using seacarb after Nisumaa et al. (2010)total scale
40 Carbon dioxideCO2µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
41 Fugacity of carbon dioxide (water) at sea surface temperature (wet air)fCO2water_SST_wetµatmYang, YanCalculated using seacarb after Nisumaa et al. (2010)
42 Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)pCO2water_SST_wetµatmYang, YanCalculated using seacarb after Nisumaa et al. (2010)
43 Bicarbonate ion[HCO3]-µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
44 Carbonate ion[CO3]2-µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
45 Aragonite saturation stateOmega ArgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
46 Calcite saturation stateOmega CalYang, YanCalculated using seacarb after Nisumaa et al. (2010)
Status:
Curation Level: Enhanced curation (CurationLevelC)
Size:
2422 data points

Data

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


Type
(study)

Species

Reg spec no

URL ref
(WoRMS Aphia ID)

Exp

Treat

Time [h]
(time post fertilization)

Ind [#]
(count, replicate 1)

Ind [#]
(partially calcified, replicate 1)
10 
Ind [#]
(fully calcified, replicate 1)
11 
Ind [#]
(count, replicate 2)
12 
Ind [#]
(partially calcified, replicate 2)
13 
Ind [#]
(fully calcified, replicate 2)
14 
Calc I
15 
Calc I std dev [±]
16 
mRNA express
17 
mRNA express std dev [±]
18 
mRNA express std e [±]
19 
mRNA express
(Tyrosinase (contig CGI_100077...)
20 
Temp [°C]
21 
Temp std dev [±]
22 
Sal
23 
Sal std dev [±]
24 
AT [µmol/kg]
25 
AT std dev [±]
26 
DIC [µmol/kg]
27 
DIC std dev [±]
28 
pCO2water_SST_wet [µatm]
29 
pCO2 std dev [±]
30 
DIC [µmol/kg]
31 
DIC std dev [±]
32 
[HCO3]- [µmol/kg]
33 
[HCO3]- std dev [±]
34 
pH
(total scale)
35 
pH std dev [±]
(total scale)
36 
Omega Arg
37 
Omega Arg std dev [±]
38 
CSC flag
39 
pH
(total scale)
40 
CO2 [µmol/kg]
41 
fCO2water_SST_wet [µatm]
42 
pCO2water_SST_wet [µatm]
43 
[HCO3]- [µmol/kg]
44 
[CO3]2- [µmol/kg]
45 
Omega Arg
46 
Omega Cal
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laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgExp.1Control12700066000.000000.0000025.80.4930.40.0022591120531356565.6188221154.711.47.920.042.530.18157.9216.26570.595721880.1156.612.563.92
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laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgExp.1Control16159277810539310.528210.0668425.80.4930.40.0022591120531356565.6188221154.711.47.920.042.530.18157.9216.26570.595721880.1156.612.563.92
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgExp.1Control18105865727330.582040.1062125.80.4930.40.0022591120531356565.6188221154.711.47.920.042.530.18157.9216.26570.595721880.1156.612.563.92
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgExp.1High CO2106900117000.000000.0000025.90.2830.40.002285142225111515104.121091072.64.57.540.031.190.07157.5443.641535.2715402107.973.471.201.84
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgExp.1High CO2121230099000.000000.0000025.90.2830.40.002285142225111515104.121091072.64.57.540.031.190.07157.5443.641535.2715402107.973.471.201.84
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgExp.1High CO214560046000.000000.0000025.90.2830.40.002285142225111515104.121091072.64.57.540.031.190.07157.5443.641535.2715402107.973.471.201.84
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgExp.1High CO216135203892580.163320.0947825.90.2830.40.002285142225111515104.121091072.64.57.540.031.190.07157.5443.641535.2715402107.973.471.201.84
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgExp.1High CO218654438217230.538230.2179025.90.2830.40.002285142225111515104.121091072.64.57.540.031.190.07157.5443.641535.2715402107.973.471.201.84
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgExp.2Control69800125000.000000.0000026.10.2330.40.0422511820031144930.8180815182.410.68.010.032.990.17158.0012.88455.334571806.6183.533.014.60
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgExp.2Control1011912054200.034470.0225626.10.2330.40.0422511820031144930.8180815182.410.68.010.032.990.17158.0012.88455.334571806.6183.533.014.60
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgExp.2Control1267110161000.041040.0580526.10.2330.40.0422511820031144930.8180815182.410.68.010.032.990.17158.0012.88455.334571806.6183.533.014.60
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgExp.2Control149027268026530.631940.2730226.10.2330.40.0422511820031144930.8180815182.410.68.010.032.990.17158.0012.88455.334571806.6183.533.014.60
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgExp.2Control1693116210913890.800980.1063126.10.2330.40.0422511820031144930.8180815182.410.68.010.032.990.17158.0012.88455.334571806.6183.533.014.60
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgExp.2Control1879670643600.942490.0260826.10.2330.40.0422511820031144930.8180815182.410.68.010.032.990.17158.0012.88455.334571806.6183.533.014.60
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgExp.2High CO261070087000.000000.0000026.30.2830.40.122284142194131242109.220711487.56.87.620.041.440.11157.6335.121247.7212522070.288.691.452.22
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgExp.2High CO2105550178700.032560.0182426.30.2830.40.122284142194131242109.220711487.56.87.620.041.440.11157.6335.121247.7212522070.288.691.452.22
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgExp.2High CO212969171400.042730.0205926.30.2830.40.122284142194131242109.220711487.56.87.620.041.440.11157.6335.121247.7212522070.288.691.452.22
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgExp.2High CO214952501759100.195790.0908126.30.2830.40.122284142194131242109.220711487.56.87.620.041.440.11157.6335.121247.7212522070.288.691.452.22
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgExp.2High CO21610948178948260.468970.1312826.30.2830.40.122284142194131242109.220711487.56.87.620.041.440.11157.6335.121247.7212522070.288.691.452.22
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgExp.2High CO218941472308202400.826060.0203226.30.2830.40.122284142194131242109.220711487.56.87.620.041.440.11157.6335.121247.7212522070.288.691.452.22
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgExp.1Control00.0413799770.0597233030.00805308825.80.4930.40.0022591120531356565.6188221154.711.47.920.042.530.18157.9216.26570.595721880.1156.612.563.92
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgExp.1Control60.0553375600.0836356890.01127743425.80.4930.40.0022591120531356565.6188221154.711.47.920.042.530.18157.9216.26570.595721880.1156.612.563.92
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgExp.1Control100.0690742030.0835303040.01126322425.80.4930.40.0022591120531356565.6188221154.711.47.920.042.530.18157.9216.26570.595721880.1156.612.563.92
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgExp.1Control120.0937677720.1085166090.01463237725.80.4930.40.0022591120531356565.6188221154.711.47.920.042.530.18157.9216.26570.595721880.1156.612.563.92
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgExp.1Control140.1779207870.1316813340.01775590725.80.4930.40.0022591120531356565.6188221154.711.47.920.042.530.18157.9216.26570.595721880.1156.612.563.92
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgExp.1Control160.4445807620.1595286040.02151083325.80.4930.40.0022591120531356565.6188221154.711.47.920.042.530.18157.9216.26570.595721880.1156.612.563.92
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgExp.1Control181.0000000000.0000000000.00000000025.80.4930.40.0022591120531356565.6188221154.711.47.920.042.530.18157.9216.26570.595721880.1156.612.563.92
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgExp.1High CO200.0413799770.0597233030.00805308825.90.2830.40.002285142225111515104.121091072.64.57.540.031.190.07157.5443.641535.2715402107.973.471.201.84
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgExp.1High CO260.0455755410.0652368490.00879653525.90.2830.40.002285142225111515104.121091072.64.57.540.031.190.07157.5443.641535.2715402107.973.471.201.84
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgExp.1High CO2100.0626974920.0725775800.00978635925.90.2830.40.002285142225111515104.121091072.64.57.540.031.190.07157.5443.641535.2715402107.973.471.201.84
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgExp.1High CO2120.0698923930.0812286890.01095287425.90.2830.40.002285142225111515104.121091072.64.57.540.031.190.07157.5443.641535.2715402107.973.471.201.84
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgExp.1High CO2140.1175332600.1049105390.01414613425.90.2830.40.002285142225111515104.121091072.64.57.540.031.190.07157.5443.641535.2715402107.973.471.201.84
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgExp.1High CO2160.2637560610.1311220700.01768049625.90.2830.40.002285142225111515104.121091072.64.57.540.031.190.07157.5443.641535.2715402107.973.471.201.84
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgExp.1High CO2180.6032249670.1324878180.01786465425.90.2830.40.002285142225111515104.121091072.64.57.540.031.190.07157.5443.641535.2715402107.973.471.201.84
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgExp.1Control00.00171114425.80.4930.40.0022591120531356565.6188221154.711.47.920.042.530.18157.9216.26570.595721880.1156.612.563.92
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgExp.1Control60.00759669925.80.4930.40.0022591120531356565.6188221154.711.47.920.042.530.18157.9216.26570.595721880.1156.612.563.92
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgExp.1Control100.53746626825.80.4930.40.0022591120531356565.6188221154.711.47.920.042.530.18157.9216.26570.595721880.1156.612.563.92
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgExp.1Control120.72437279525.80.4930.40.0022591120531356565.6188221154.711.47.920.042.530.18157.9216.26570.595721880.1156.612.563.92
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laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgExp.1High CO260.00564254325.90.2830.40.002285142225111515104.121091072.64.57.540.031.190.07157.5443.641535.2715402107.973.471.201.84
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgExp.1High CO2100.46111683025.90.2830.40.002285142225111515104.121091072.64.57.540.031.190.07157.5443.641535.2715402107.973.471.201.84
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgExp.1High CO2121.00000000025.90.2830.40.002285142225111515104.121091072.64.57.540.031.190.07157.5443.641535.2715402107.973.471.201.84
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgExp.1High CO2140.68600698625.90.2830.40.002285142225111515104.121091072.64.57.540.031.190.07157.5443.641535.2715402107.973.471.201.84
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgExp.1High CO2160.34627515525.90.2830.40.002285142225111515104.121091072.64.57.540.031.190.07157.5443.641535.2715402107.973.471.201.84
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgExp.1High CO2180.19840866725.90.2830.40.002285142225111515104.121091072.64.57.540.031.190.07157.5443.641535.2715402107.973.471.201.84
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgExp.2Control00.00422037326.10.2330.40.0422511820031144930.8180815182.410.68.010.032.990.17158.0012.88455.334571806.6183.533.014.60
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgExp.2Control60.00199486826.10.2330.40.0422511820031144930.8180815182.410.68.010.032.990.17158.0012.88455.334571806.6183.533.014.60
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgExp.2Control100.61155350226.10.2330.40.0422511820031144930.8180815182.410.68.010.032.990.17158.0012.88455.334571806.6183.533.014.60
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgExp.2Control120.94337281126.10.2330.40.0422511820031144930.8180815182.410.68.010.032.990.17158.0012.88455.334571806.6183.533.014.60
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgExp.2Control140.24698652326.10.2330.40.0422511820031144930.8180815182.410.68.010.032.990.17158.0012.88455.334571806.6183.533.014.60
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgExp.2Control160.21738791226.10.2330.40.0422511820031144930.8180815182.410.68.010.032.990.17158.0012.88455.334571806.6183.533.014.60
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgExp.2Control180.08235775326.10.2330.40.0422511820031144930.8180815182.410.68.010.032.990.17158.0012.88455.334571806.6183.533.014.60
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgExp.2High CO200.00422037326.30.2830.40.122284142194131242109.220711487.56.87.620.041.440.11157.6335.121247.7212522070.288.691.452.22
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgExp.2High CO260.00346550126.30.2830.40.122284142194131242109.220711487.56.87.620.041.440.11157.6335.121247.7212522070.288.691.452.22
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgExp.2High CO2101.00000000026.30.2830.40.122284142194131242109.220711487.56.87.620.041.440.11157.6335.121247.7212522070.288.691.452.22
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgExp.2High CO2120.70393486126.30.2830.40.122284142194131242109.220711487.56.87.620.041.440.11157.6335.121247.7212522070.288.691.452.22
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgExp.2High CO2140.57803115726.30.2830.40.122284142194131242109.220711487.56.87.620.041.440.11157.6335.121247.7212522070.288.691.452.22
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgExp.2High CO2160.22103689426.30.2830.40.122284142194131242109.220711487.56.87.620.041.440.11157.6335.121247.7212522070.288.691.452.22
laboratoryCrassostrea gigas (mollusk)140656marinespecies.orgExp.2High CO2180.09716213726.30.2830.40.122284142194131242109.220711487.56.87.620.041.440.11157.6335.121247.7212522070.288.691.452.22