Citation:

PANGAEA.945551

Name: Seawater carbonate chemistry and gene expression stability of Hong Kong oyster (Crassostrea hongkongensis)
Published: 2022-06-21
License: https://creativecommons.org/licenses/by/4.0/
Keywords: Animalia; Benthic animals; Benthos; Coast and continental shelf; Containers and aquaria (20-1000 L or < 1 m**2); Gene expression (incl. proteomics); Laboratory experiment; Magallana hongkongensis; Mollusca; North Pacific; Single species; Tropical

Always quote citation above when using data! You can download the citation in several formats below.

RIS Citation BibTeX Citation Text Citation Facebook TwitterShow Map Google Earth

Abstract:

The increase of CO2 by anthropogenic activities leads to a decrease of pH in the ocean surface due to ocean acidification (OA) process. Generally, OA not only reduces the rate of calcification in marine environments but also affects various physiological activities, especially in calcifiers, including edible oysters. Quantitative real-time PCR (qRT-PCR) is often used to detect gene expression in response to OA, which relies on the stability of internal control. However, the appropriate internal controls for OA experiments remain scarce especially in the marine calcifiers. Hence, this study developed internal controls for qRT-PCR assays using the Hong Kong oyster (Crassostrea hongkongensis) as a model to reveal gene expression profile during development under OA. In this study, 17 housekeeping genes were selected as the possible candidate of the internal controls. After a comprehensive interpretation from the multiple algorithms and software, GAPDH paired with RL23 is recommended for the normalization for planktonic larvae and benthic juveniles, but beyond that, TUBB and EF2 are recommended for post-metamorphic stage. Moreover, GAPDH and EF2 were suitable for various pH treatments, and TUBB, RL35 and RL23 could be the alternatives for OA experiments. These results are instrumental for the selection of internal control in Crassostrea hongkongensis during the development, and shed light on other molecular OA experiments in marine invertebrates for reference.

Keyword(s):

Animalia; Benthic animals; Benthos; Coast and continental shelf; Containers and aquaria (20-1000 L or < 1 m**2); Gene expression (incl. proteomics); Laboratory experiment; Magallana hongkongensis; Mollusca; North Pacific; Single species; Tropical

Supplement to:

Dang, Xin; Noor, Zohaib; He, Yuanqiu; Lim, Yong Kian; Zhang, Yang; Yu, Ziniu; Thiyagarajan, Vengatesen (2022): Internal controls for quantitative RT-PCR analysis of gene expression in response to ocean acidification in edible oysters. Journal of Experimental Marine Biology and Ecology, 548, 151683, https://doi.org/10.1016/j.jembe.2021.151683

Further details:

Gattuso, Jean-Pierre; Epitalon, Jean-Marie; Lavigne, Héloïse; Orr, James (2021): seacarb: seawater carbonate chemistry with R. R package version 3.2.16. https://cran.r-project.org/web/packages/seacarb/index.html

Project(s):

Ocean Acidification International Coordination Centre (OA-ICC)

Coverage:

Latitude: 21.590000 * Longitude: 108.980000

Event(s):

Beihai_OA * Latitude: 21.590000 * Longitude: 108.980000 * Method/Device: Experiment (EXP)

Comment:

In order to allow full comparability with other ocean acidification data sets, the R package seacarb (Gattuso et al, 2021) 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 2022-06-20.

The species name used in the paper is Crassostrea hongkongensis.

Parameter(s):

#	Name	Short Name	Unit	Principal Investigator	Method/Device	Comment
1	Type	Type		Thiyagarajan, Vengatesen		Study
2	Species, unique identification	Species UID		Thiyagarajan, Vengatesen
3	Species, unique identification (URI)	Species UID (URI)		Thiyagarajan, Vengatesen
4	Species, unique identification (Semantic URI)	Species UID (Semantic URI)		Thiyagarajan, Vengatesen
5	Treatment	Treat		Thiyagarajan, Vengatesen
6	Gene name	Gene		Thiyagarajan, Vengatesen
7	Stability	Stability		Thiyagarajan, Vengatesen		M value generated by GeNorm
8	Stability	Stability		Thiyagarajan, Vengatesen		generated by NormFinder
9	pH	pH		Thiyagarajan, Vengatesen		NBS scale, Pediveliger larvae (23 dpf)
10	Temperature, water	Temp	°C	Thiyagarajan, Vengatesen		Pediveliger larvae (23 dpf)
11	Salinity	Sal		Thiyagarajan, Vengatesen		Pediveliger larvae (23 dpf)
12	Alkalinity, total	AT	µmol/kg	Thiyagarajan, Vengatesen		Pediveliger larvae (23 dpf)
13	pH	pH		Thiyagarajan, Vengatesen		NBS scale, Postmetamorphic spats (30dpf)
14	Temperature, water	Temp	°C	Thiyagarajan, Vengatesen		Postmetamorphic spats (30dpf)
15	Salinity	Sal		Thiyagarajan, Vengatesen		Postmetamorphic spats (30dpf)
16	Alkalinity, total	AT	µmol/kg	Thiyagarajan, Vengatesen		Postmetamorphic spats (30dpf)
17	pH	pH		Thiyagarajan, Vengatesen		NBS scale, Juveniles (3 month)
18	Temperature, water	Temp	°C	Thiyagarajan, Vengatesen		Juveniles (3 month)
19	Salinity	Sal		Thiyagarajan, Vengatesen		Juveniles (3 month)
20	Alkalinity, total	AT	µmol/kg	Thiyagarajan, Vengatesen		Juveniles (3 month)
21	Carbonate system computation flag	CSC flag		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
22	pH	pH		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	Total scale, Pediveliger larvae (23 dpf)
23	Carbon dioxide	CO2	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	Pediveliger larvae (23 dpf)
24	Fugacity of carbon dioxide (water) at sea surface temperature (wet air)	fCO2water_SST_wet	µatm	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	Pediveliger larvae (23 dpf)
25	Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)	pCO2water_SST_wet	µatm	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	Pediveliger larvae (23 dpf)
26	Bicarbonate ion	[HCO3]-	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	Pediveliger larvae (23 dpf)
27	Carbonate ion	[CO3]2-	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	Pediveliger larvae (23 dpf)
28	Carbon, inorganic, dissolved	DIC	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	Pediveliger larvae (23 dpf)
29	Aragonite saturation state	Omega Arg		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	Pediveliger larvae (23 dpf)
30	Calcite saturation state	Omega Cal		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	Pediveliger larvae (23 dpf)
31	pH	pH		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	Total scale, Postmetamorphic spats (30dpf)
32	Carbon dioxide	CO2	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	Postmetamorphic spats (30dpf)
33	Fugacity of carbon dioxide (water) at sea surface temperature (wet air)	fCO2water_SST_wet	µatm	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	Postmetamorphic spats (30dpf)
34	Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)	pCO2water_SST_wet	µatm	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	Postmetamorphic spats (30dpf)
35	Bicarbonate ion	[HCO3]-	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	Postmetamorphic spats (30dpf)
36	Carbonate ion	[CO3]2-	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	Postmetamorphic spats (30dpf)
37	Carbon, inorganic, dissolved	DIC	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	Postmetamorphic spats (30dpf)
38	Aragonite saturation state	Omega Arg		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	Postmetamorphic spats (30dpf)
39	Calcite saturation state	Omega Cal		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	Postmetamorphic spats (30dpf)
40	pH	pH		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	Total scale, Juveniles (3 month)
41	Carbon dioxide	CO2	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	Juveniles (3 month)
42	Fugacity of carbon dioxide (water) at sea surface temperature (wet air)	fCO2water_SST_wet	µatm	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	Juveniles (3 month)
43	Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)	pCO2water_SST_wet	µatm	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	Juveniles (3 month)
44	Bicarbonate ion	[HCO3]-	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	Juveniles (3 month)
45	Carbonate ion	[CO3]2-	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	Juveniles (3 month)
46	Carbon, inorganic, dissolved	DIC	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	Juveniles (3 month)
47	Aragonite saturation state	Omega Arg		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	Juveniles (3 month)
48	Calcite saturation state	Omega Cal		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	Juveniles (3 month)

License:

Creative Commons Attribution 4.0 International (CC-BY-4.0)

Status:

Curation Level: Enhanced curation (CurationLevelC)

Size:

4590 data points

Download Data

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

View dataset as HTML (shows only first 2000 rows)