Seawater carbonate chemistry and gene expression, shell formation in larval Pacific oysters (Crassostrea gigas), supplement to: de Wit, Pierre; Durland, Evan; Ventura, Alexander; Langdon, Chris (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)

DOI

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.

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.

Identifier
DOI https://doi.org/10.1594/PANGAEA.893428
Related Identifier https://doi.org/10.1186/s12864-018-4519-y
Related Identifier https://store.pangaea.de/Publications/DeWit-etal_2018/Weighted_gene_correlation_network_modules_and_normalized_expression_levels.xlsx
Related Identifier https://cran.r-project.org/package=seacarb
Metadata Access https://ws.pangaea.de/oai/provider?verb=GetRecord&metadataPrefix=datacite4&identifier=oai:pangaea.de:doi:10.1594/PANGAEA.893428
Provenance
Creator de Wit, Pierre; Durland, Evan; Ventura, Alexander; Langdon, Chris
Publisher PANGAEA - Data Publisher for Earth & Environmental Science
Contributor Yang, Yan
Publication Year 2018
Rights Creative Commons Attribution 3.0 Unported; https://creativecommons.org/licenses/by/3.0/
OpenAccess true
Representation
Language English
Resource Type Supplementary Dataset; Dataset
Format text/tab-separated-values
Size 2422 data points
Discipline Earth System Research