10.5061/DRYAD.8M5V4
De Wit, Pierre
University of Gothenburg
Durland, Evan
Newport (United States)
Ventura, Alexander
University of Gothenburg
Langdon, Chris J.
Newport (United States)
Data from: 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
Dryad
dataset
2019
Aragonite
Larvae
Calcification
Crassostrea gigas
2019-01-31T00:00:00Z
2019-01-31T00:00:00Z
en
https://doi.org/10.1186/s12864-018-4519-y
11000706 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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 hours 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
pCO2-acidified seawater to identify genes correlated with initial shell
deposition. 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. 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.
Experiment 1 (NET3) Raw read counts (with duplicates)Experiment 1 (NET3)
Raw read counts (with duplicates), mapped to the oyster genome v9 coding
regions.NET3_Counts_with_dups.txtExperiment 2 (NET1) Raw read counts (with
duplicates)Experiment 2 (NET1) Raw read counts (with duplicates), mapped
against the oyster genome v9 coding
regions.NET1_Counts_with_dups.txtExperiment 1 (NET3) Raw read counts
(duplicates removed)Experiment 1 (NET3) Raw read counts (duplicates
removed), mapped against the oyster genome v9 coding
regionsNET3_Counts_dedup.txtExperiment 2 (NET1) Raw read counts
(duplicates removed)Experiment 2 (NET1) Raw read counts (duplicates
removed), mapped against the oyster genome v9 coding
regionsNET1_Counts_dedup.txtSupporting information - ErmineJ Functional
enrichment results fileSupporting information - ErmineJ Functional
enrichment results fileSI_TableS2_ERMINEJ GSR runs.project