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Differential gene expression reveals molecular mechanisms for physiological resilience to ocean acidification stress in native and introduced oyster species

https://doi.org/10.2139/ssrn.7445848
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Carryover effects of temperature and pCO 2 across multiple Olympia oyster populations
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Meta‐analysis suggests negative, but pCO2‐specific, effects of ocean acidification on the structural and functional properties of crustacean biomaterials
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Living in a high CO 2 world: a global meta‐analysis shows multiple trait‐mediated fish responses to ocean acidification
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Comparative and quantitative proteomics reveal the adaptive strategies of oyster larvae to ocean acidification
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Impacts of ocean acidification on marine shelled molluscs
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Calcineurin Plays an Important Role in the Shell Formation of Pearl Oyster (Pinctada fucata)
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Population dynamics of the invasive Pacific oyster Crassostrea gigas during the early stages of an outbreak in the Wadden Sea (Germany)
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Calcium carbonate saturation and ocean acidification in Tokyo Bay, Japan
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A novel extracellular EF-hand protein involved in the shell formation of pearl oyster
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Molluscan shell evolution with review of shell calcification hypothesis
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The combined effects of ocean acidification, mixing, and respiration on pH and carbonate saturation in an urbanized estuary
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Effects of ocean acidification on immune responses of the Pacific oyster Crassostrea gigas
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The impact of ocean acidification and cadmium on the immune responses of Pacific oyster, Crassostrea gigas
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Molecular basis of ocean acidification sensitivity and adaptation in Mytilus galloprovincialis
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Effects of sea-water acidification on fertilization and larval development of the oyster Crassostrea gigas
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Linking the biological impacts of ocean acidification on oysters to changes in ecosystem services: A review
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Indications of future performance of native and non-native adult oysters under acidification and warming
inferredcites →https://doi.org/10.1016/j.marenvres.2022.105709openalex-snapshot
Harsh intertidal environment enhances metabolism and immunity in oyster (Crassostrea gigas) spat
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Ocean acidification impacts on coral reefs: From sciences to solutions
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Transcriptional changes of Pacific oyster Crassostrea gigas reveal essential role of calcium signal pathway in response to CO2-driven acidification
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Anthropogenic carbon and ocean pH
inferredcites →https://doi.org/10.1038/75556openalex-snapshot
Gene Ontology: tool for the unification of biology
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Anthropogenic ocean acidification over the twenty-first century and its impact on calcifying organisms
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The oyster genome reveals stress adaptation and complexity of shell formation
inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot
Fast gapped-read alignment with Bowtie 2
inferredcites →https://doi.org/10.1038/nmeth.4197openalex-snapshot
Salmon provides fast and bias-aware quantification of transcript expression
inferredcites →https://doi.org/10.1038/s41467-019-13767-1openalex-snapshot
Standing genetic variation fuels rapid adaptation to ocean acidification
inferredcites →https://doi.org/10.1038/s41559-017-0084openalex-snapshot
Species-specific responses to ocean acidification should account for local adaptation and adaptive plasticity
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Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype
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Using clusterProfiler to characterize multiomics data
inferredcites →https://doi.org/10.1038/s41598-020-69568-wopenalex-snapshot
Temperature and salinity, not acidification, predict near-future larval growth and larval habitat suitability of Olympia oysters in the Salish Sea
inferredcites →https://doi.org/10.1038/s43247-023-01065-0openalex-snapshot
A 37-year record of ocean acidification in the Southern California current
inferredcites →https://doi.org/10.1073/pnas.1416967112openalex-snapshot
Experimental ocean acidification alters the allocation of metabolic energy
inferredcites →https://doi.org/10.1073/pnas.1703445115openalex-snapshot
Seagrass habitat metabolism increases short-term extremes and long-term offset of CO 2 under future ocean acidification
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Evolved differences in energy metabolism and growth dictate the impacts of ocean acidification on abalone aquaculture
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Impacts of a bivalve mass mortality event on an estuarine food web and bivalve grazing pressure
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CD-HIT: accelerated for clustering the next-generation sequencing data
inferredcites →https://doi.org/10.1093/bioinformatics/btt656openalex-snapshot
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
inferredcites →https://doi.org/10.1093/bioinformatics/btu170openalex-snapshot
Trimmomatic: a flexible trimmer for Illumina sequence data
inferredcites →https://doi.org/10.1093/bioinformatics/btw354openalex-snapshot
MultiQC: summarize analysis results for multiple tools and samples in a single report
inferredcites →https://doi.org/10.1093/icb/42.4.780openalex-snapshot
Thermal Physiology and Vertical Zonation of Intertidal Animals: Optima, Limits, and Costs of Living
inferredcites →https://doi.org/10.1093/icesjms/fsw213openalex-snapshot
Metabolic cost of calcification in bivalve larvae under experimental ocean acidification
inferredcites →https://doi.org/10.1093/molbev/msab199openalex-snapshot
BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes
inferredcites →https://doi.org/10.1101/gr.234807.118openalex-snapshot
Gene expression profiling of single cells from archival tissue with laser-capture microdissection and Smart-3SEQ
inferredcites →https://doi.org/10.1111/eva.12766openalex-snapshot
Population structure, genetic connectivity, and adaptation in the Olympia oyster ( Ostrea lurida ) along the west coast of North America
inferredcites →https://doi.org/10.1111/eva.13289openalex-snapshot
Larval development in the Pacific oyster and the impacts of ocean acidification: Differential genetic effects in wild and domesticated stocks
inferredcites →https://doi.org/10.1111/gcb.12307openalex-snapshot
Larval carry‐over effects from ocean acidification persist in the natural environment
inferredcites →https://doi.org/10.1111/gcb.15675openalex-snapshot
Oyster biomineralization under ocean acidification: From genes to shell
inferredcites →https://doi.org/10.1111/gcb.16101openalex-snapshot
Revisiting tolerance to ocean acidification: Insights from a new framework combining physiological and molecular tipping points of Pacific oyster
inferredcites →https://doi.org/10.1111/j.1365-2435.2012.02061.xopenalex-snapshot
Adaptation and the physiology of ocean acidification
inferredcites →https://doi.org/10.1111/j.1461-0248.2010.01518.xopenalex-snapshot
Meta‐analysis reveals negative yet variable effects of ocean acidification on marine organisms
inferredcites →https://doi.org/10.1111/j.1467-2979.2011.00424.xopenalex-snapshot
Nutrition and income from molluscs today imply vulnerability to ocean acidification tomorrow
inferredcites →https://doi.org/10.1111/mec.14333openalex-snapshot
Transcriptomic profiling of adaptive responses to ocean acidification
inferredcites →https://doi.org/10.1111/mec.14863openalex-snapshot
Transcriptomic responses to extreme low salinity among locally adapted populations of Olympia oyster (Ostrea lurida)
inferredcites →https://doi.org/10.1126/science.1097329openalex-snapshot
Impact of Anthropogenic CO 2 on the CaCO 3 System in the Oceans
inferredcites →https://doi.org/10.1126/science.1097403openalex-snapshot
The Oceanic Sink for Anthropogenic CO 2
inferredcites →https://doi.org/10.1126/science.1155676openalex-snapshot
Evidence for Upwelling of Corrosive "Acidified" Water onto the Continental Shelf
inferredcites →https://doi.org/10.1146/annurev-environ-012320-083019openalex-snapshot
The Impacts of Ocean Acidification on Marine Ecosystems and Reliant Human Communities
inferredcites →https://doi.org/10.1146/annurev-marine-121211-172241openalex-snapshot
Ocean Acidification and Coral Reefs: Effects on Breakdown, Dissolution, and Net Ecosystem Calcification
inferredcites →https://doi.org/10.1146/annurev.ecolsys.36.102003.152638openalex-snapshot
Introduction of Non-Native Oysters: Ecosystem Effects and Restoration Implications
inferredcites →https://doi.org/10.1146/annurev.marine.010908.163834openalex-snapshot
Ocean Acidification: The Other CO 2 Problem
inferredcites →https://doi.org/10.1152/ajpregu.00064.2014openalex-snapshot
Physiological impacts of elevated carbon dioxide and ocean acidification on fish
inferredcites →https://doi.org/10.1186/1756-0500-5-502openalex-snapshot
Characterization of genes involved in ceramide metabolism in the Pacific oyster (Crassostrea gigas)
inferredcites →https://doi.org/10.1186/s12864-018-4519-yopenalex-snapshot
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
inferredcites →https://doi.org/10.1186/s12983-020-0350-9openalex-snapshot
Ocean acidification promotes broad transcriptomic responses in marine metazoans: a literature survey
inferredcites →https://doi.org/10.1371/journal.pone.0021860openalex-snapshot
Identification of Genes Directly Involved in Shell Formation and Their Functions in Pearl Oyster, Pinctada fucata
inferredcites →https://doi.org/10.1371/journal.pone.0046244openalex-snapshot
Transcriptomic Responses to Salinity Stress in the Pacific Oyster Crassostrea gigas
inferredcites →https://doi.org/10.1371/journal.pone.0252810openalex-snapshot
Conservation aquaculture as a tool for imperiled marine species: Evaluation of opportunities and risks for Olympia oysters, Ostrea lurida
inferredcites →https://doi.org/10.1371/journal.pone.0263998openalex-snapshot
Mapping oysters on the Pacific coast of North America: A coast-wide collaboration to inform enhanced conservation
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Economic Valuation of Ecosystem Services Provided by Oyster Reefs
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The Nearly Forgotten Oyster:Ostrea luridaCarpenter 1864 (Olympia Oyster) History and Management in Washington State
inferredcites →https://doi.org/10.2983/035.028.0111openalex-snapshot
History of Olympia Oysters (Ostrea luridaCarpenter 1864) in Oregon Estuaries, and a Description of Recovering Populations in Coos Bay
inferredcites →https://doi.org/10.2983/035.028.0112openalex-snapshot
Status of the Olympia Oyster,Ostrea luridaCarpenter 1864, in British Columbia, Canada
inferredcites →https://doi.org/10.2983/035.028.0113openalex-snapshot
Geographic Distribution and Intertidal Population Status for the Olympia Oyster,Ostrea luridaCarpenter 1864, from Alaska to Baja
inferredcites →https://doi.org/10.2983/035.028.0116openalex-snapshot
Factors Preventing the Recovery of a Historically Overexploited Shellfish Species,Ostrea luridaCarpenter 1864
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The Olympia OysterOstrea lurida: Recent Advances in Natural History, Ecology, and Restoration
inferredcites →https://doi.org/10.3354/meps07802openalex-snapshot
Effects of CO2-driven ocean acidification on the early developmental stages of invertebrates
inferredcites →https://doi.org/10.3354/meps09185openalex-snapshot
Physiological and ecological responses of crustaceans to ocean acidification
inferredcites →https://doi.org/10.3354/meps13687openalex-snapshot
Differential responses in anti-predation traits of the native oyster Ostrea edulis and invasive Magallana gigas to ocean acidification and warming
inferredcites →https://doi.org/10.3389/fmars.2020.597441openalex-snapshot
How the Pacific Oyster Responds to Ocean Acidification: Development and Application of a Meta-Analysis Based Adverse Outcome Pathway
inferredcites →https://doi.org/10.3389/fmars.2021.782583openalex-snapshot
Ocean Acidification Triggers Cell Signaling, Suppress Immune and Calcification in the Pacific Oyster Larvae
inferredcites →https://doi.org/10.3389/fphys.2021.647482openalex-snapshot
Single-Larva RNA Sequencing Identifies Markers of Copper Toxicity and Exposure in Early Mytilus californianus Larvae
inferredcites →https://doi.org/10.3390/ijms16011406openalex-snapshot
Structure and Function of SET and MYND Domain-Containing Proteins
inferredcites →https://doi.org/10.4236/ajmb.2018.84018openalex-snapshot
Ca2+-Induced Conformational Change of Troponin C from the Japanese Pearl Oyster, Pinctada fucata
inferredcites →https://doi.org/10.4319/lo.2012.57.3.0698openalex-snapshot
The Pacific oyster, Crassostrea gigas , shows negative correlation to naturally elevated carbon dioxide levels: Implications for near‐term ocean acidification effects
inferredcites →https://doi.org/10.5194/bg-7-2051-2010openalex-snapshot
Effect of ocean acidification on the early life stages of the blue mussel Mytilus edulis
inferredcites →https://doi.org/10.5194/bg-8-919-2011openalex-snapshot
Impact of ocean acidification and elevated temperatures on early juveniles of the polar shelled pteropod Limacina helicina : mortality, shell degradation, and shell growth
inferredcites →https://doi.org/10.5670/oceanog.2009.97openalex-snapshot
OCEAN ACIDIFICATION IN THE CALIFORNIA CURRENT SYSTEM
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