Combination of RNAseq and RADseq to Identify Physiological and Adaptive Responses to Acidification in the Eastern Oyster (Crassostrea virginica)

RNAi Silencing of the Biomineralization Gene Perlucin Impairs Oyster Ability to Cope with Ocean Acidification

(2023) Caroline Schwaner et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Analysing high-throughput sequencing data in Python with HTSeq 2.0

(2022) Givanna H Putri et al.   BIOINFORMATICS

Chromosomal assembly of the flat oyster ( Ostrea edulis L.) genome as a new genetic resource for aquaculture

(2022) Isabelle Boutet et al.   Evolutionary Applications

A Transcriptomic Analysis of Phenotypic Plasticity in Crassostrea virginica Larvae under Experimental Acidification

(2022) Michelle Barbosa et al.   Genes

Transcriptomic Response of Mussel Gills After a Vibrio splendidus Infection Demonstrates Their Role in the Immune Response

(2021) Amaro Saco et al.   Frontiers in Immunology

Acidification stress effect on umbonate veliger larval development in Panopea globosa

(2021) Edgar A. López-Landavery et al.   MARINE POLLUTION BULLETIN

SambaR: An R package for fast, easy and reproducible population‐genetic analyses of biallelic SNP data sets

(2021) Menno J. Jong et al.   Molecular Ecology Resources

Oyster biomineralisation under ocean acidification: from genes to shell

(2021) Kanmani Chandra Rajan et al.   GLOBAL CHANGE BIOLOGY

Harnessing the power of multi‐omics data for predicting climate change response

(2021) Kara K. S. Layton et al.   JOURNAL OF ANIMAL ECOLOGY

Ocean acidification promotes broad transcriptomic responses in marine metazoans: a literature survey

(2020) Marie E. Strader et al.   Frontiers in Zoology

Molecular adaptation of molluscan biomineralisation to high-CO2 oceans – The known and the unknown

(2020) Kanmani Chandra Rajan et al.   MARINE ENVIRONMENTAL RESEARCH

A tandem-repeat galectin-1 from Apostichopus japonicus with broad PAMP recognition pattern and antibacterial activity

(2020) Chi Zhang et al.   FISH & SHELLFISH IMMUNOLOGY

Regulation of ion transport and energy metabolism enables certain coral genotypes to maintain calcification under experimental ocean acidification

(2020) Amanda Glazier et al.   MOLECULAR ECOLOGY

Magnitude and predictability of pH fluctuations shape plastic responses to ocean acidification

(2020) Mark Bitter et al.   AMERICAN NATURALIST

In Silico Analysis of Pacific Oyster (Crassostrea gigas) Transcriptome over Developmental Stages Reveals Candidate Genes for Larval Settlement

(2019) Valentin Foulon et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Differential responses to ocean acidification between populations of Balanophyllia elegans corals from high and low upwelling environments

(2019) Joanna S. Griffiths et al.   MOLECULAR ECOLOGY

Recommended priorities for research on ecological impacts of ocean and coastal acidification in the U.S. Mid-Atlantic

(2019) Grace K. Saba et al.   ESTUARINE COASTAL AND SHELF SCIENCE

Stacks 2: analytical methods for paired‐end sequencing improve RADseq‐based population genomics

(2019) Nicolas C. Rochette et al.   MOLECULAR ECOLOGY

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

Little evidence of adaptation potential to ocean acidification in sea urchins living in “Future Ocean” conditions at a CO 2 vent

(2019) Sven Uthicke et al.   Ecology and Evolution

Evaluation of protein requirement of spotted seabass (Lateolabrax maculatus) under two temperatures, and the liver transcriptome response to thermal stress

(2019) Lin-Sen Cai et al.   AQUACULTURE

CO2-driven ocean acidification weakens mussel shell defense capacity and induces global molecular compensatory responses

(2019) Xinguo Zhao et al.   CHEMOSPHERE

Standing genetic variation fuels rapid adaptation to ocean acidification

(2019) M. C. Bitter et al.   Nature Communications

Identifying Genes Whose Mutant Transcripts Cause Dominant Disease Traits by Potential Gain-of-Function Alleles

(2018) Zeynep Coban-Akdemir et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

(2018) Pierre De Wit et al.   BMC GENOMICS

Long-term affected flat oyster ( Ostrea edulis ) haemocytes show differential gene expression profiles from naïve oysters in response to Bonamia ostreae

(2018) P. Ronza et al.   GENOMICS

Eater and draper are involved in the periostial haemocyte immune response in the mosquito Anopheles gambiae

(2018) L. T. Sigle et al.   INSECT MOLECULAR BIOLOGY

Transcriptomic analysis of embryo development in the invasive snail Pomacea canaliculata

(2018) Yaming Xiong et al.   JOURNAL OF MOLLUSCAN STUDIES

CO 2 -induced ocean acidification impairs the immune function of the Pacific oyster against Vibrio splendidus challenge: An integrated study from a cellular and proteomic perspective

(2018) Ruiwen Cao et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Ocean Acidification Affects the Cytoskeleton, Lysozymes, and Nitric Oxide of Hemocytes: A Possible Explanation for the Hampered Phagocytosis in Blood Clams, Tegillarca granosa

(2018) Wenhao Su et al.   Frontiers in Physiology

OUP accepted manuscript

(2018)   DNA RESEARCH

Insights into the evolution of shells and love darts of land snails revealed from their matrix proteins

(2018) Keisuke Shimizu et al.   Genome Biology and Evolution

Ocean pH fluctuations affect mussel larvae at key developmental transitions

(2018) L. Kapsenberg et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Differentially expressed immune-related genes in hemocytes of the pearl oyster Pinctada fucata against allograft identified by transcriptome analysis

(2017) Jinfen Wei et al.   FISH & SHELLFISH IMMUNOLOGY

Ocean acidification and pathogen exposure modulate the immune response of the edible mussel Mytilus chilensis

(2017) Nicole Castillo et al.   FISH & SHELLFISH IMMUNOLOGY

An approach to the study of the immunity functions of bivalve haemocytes: Physiology and molecular aspects

(2017) Mario Alberto Burgos-Aceves et al.   FISH & SHELLFISH IMMUNOLOGY

Deep conservation of bivalve nacre proteins highlighted by shell matrix proteomics of the UnionoidaElliptio complanataandVillosa lienosa

(2017) Benjamin Marie et al.   Journal of the Royal Society Interface

Ocean acidification adversely influences metabolism, extracellular pH and calcification of an economically important marine bivalve, Tegillarca granosa

(2017) Xinguo Zhao et al.   MARINE ENVIRONMENTAL RESEARCH

Transcriptomic profiling of adaptive responses to ocean acidification

(2017) Priscila Goncalves et al.   MOLECULAR ECOLOGY

Naturally acidified habitat selects for ocean acidification–tolerant mussels

(2017) Jörn Thomsen et al.   Science Advances

Exposure to low pH induces molecular level changes in the marine worm, Platynereis dumerilii

(2016) Janine Wäge et al.   ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY

Effects of ocean acidification on immune responses of the Pacific oyster Crassostrea gigas

(2016) Qing Wang et al.   FISH & SHELLFISH IMMUNOLOGY

Ocean acidification weakens the immune response of blood clam through hampering the NF-kappa β and toll-like receptor pathways

(2016) Saixi Liu et al.   FISH & SHELLFISH IMMUNOLOGY

Sea shell diversity and rapidly evolving secretomes: insights into the evolution of biomineralization

(2016) Kevin M. Kocot et al.   Frontiers in Zoology

Biomineralization changes with food supply confer juvenile scallops (Argopecten purpuratus) resistance to ocean acidification

(2016) Laura Ramajo et al.   GLOBAL CHANGE BIOLOGY

Near-future pH conditions severely impact calcification, metabolism and the nervous system in the pteropodHeliconoides inflatus

(2016) Aurelie Moya et al.   GLOBAL CHANGE BIOLOGY

Metabolic cost of calcification in bivalve larvae under experimental ocean acidification

(2016) Christina A. Frieder et al.   ICES JOURNAL OF MARINE SCIENCE

Insights from the Shell Proteome: Biomineralization to Adaptation

(2016) Jaison Arivalagan et al.   MOLECULAR BIOLOGY AND EVOLUTION

Rapid transcriptional acclimation following transgenerational exposure of oysters to ocean acidification

(2016) Priscila Goncalves et al.   MOLECULAR ECOLOGY

pcadapt: anRpackage to perform genome scans for selection based on principal component analysis

(2016) Keurcien Luu et al.   Molecular Ecology Resources

Sequencing, De Novo Assembly, and Annotation of the Transcriptome of the Endangered Freshwater Pearl Bivalve, Cristaria plicata, Provides Novel Insights into Functional Genes and Marker Discovery

(2016) Bharat Bhusan Patnaik et al.   PLoS One

Molecular Basis for Adaptation of Oysters to Stressful Marine Intertidal Environments

(2016) Guofan Zhang et al.   Annual Review of Animal Biosciences

Transcriptome and biomineralization responses of the pearl oyster Pinctada fucata to elevated CO2 and temperature

(2016) Shiguo Li et al.   Scientific Reports

Reliable Detection of Loci Responsible for Local Adaptation: Inference of a Null Model through Trimming the Distribution of FST

(2015) Michael C. Whitlock et al.   AMERICAN NATURALIST

Morphology and classification of hemocytes in Pinctada fucata and their responses to ocean acidification and warming

(2015) Shiguo Li et al.   FISH & SHELLFISH IMMUNOLOGY

Rapid acclimation of juvenile corals to CO2-mediated acidification by upregulation of heat shock protein and Bcl-2 genes

(2015) A. Moya et al.   MOLECULAR ECOLOGY

Experimental ocean acidification alters the allocation of metabolic energy

(2015) T.-C. Francis Pan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparative and quantitative proteomics reveal the adaptive strategies of oyster larvae to ocean acidification

(2015) R. Dineshram et al.   PROTEOMICS

Shotgun proteomics reveals physiological response to ocean acidification in Crassostrea gigas

(2014) Emma Timmins-Schiffman et al.   BMC GENOMICS

Molecular mechanisms underlying the physiological responses of the cold-water coral Desmophyllum dianthus to ocean acidification

(2014) M. Carreiro-Silva et al.   CORAL REEFS

Multilocus Adaptation Associated with Heat Resistance in Reef-Building Corals

(2014) Rachael A. Bay et al.   CURRENT BIOLOGY

Large Natural pH, CO2 and O2 Fluctuations in a Temperate Tidal Salt Marsh on Diel, Seasonal, and Interannual Time Scales

(2014) Hannes Baumann et al.   Estuaries and Coasts

Coastal ocean acidification: The other eutrophication problem

(2014) Ryan B. Wallace et al.   ESTUARINE COASTAL AND SHELF SCIENCE

Deep transcriptome sequencing of Pecten maximus hemocytes: A genomic resource for bivalve immunology

(2014) Marianna Pauletto et al.   FISH & SHELLFISH IMMUNOLOGY

Adaptation of a globally important coccolithophore to ocean warming and acidification

(2014) Lothar Schlüter et al.   Nature Climate Change

Physiological response and resilience of early life-stage Eastern oysters (Crassostrea virginica) to past, present and future ocean acidification

(2014) C. J. Gobler et al.   Conservation Physiology

Ocean Acidification in the Coastal Zone from an Organism's Perspective: Multiple System Parameters, Frequency Domains, and Habitats

(2013) George G. Waldbusser et al.   Annual Review of Marine Science

Mollusk shell structures and their formation mechanism

(2013) Michio Suzuki et al.   CANADIAN JOURNAL OF ZOOLOGY

Climate change in the oceans: evolutionary versus phenotypically plastic responses of marine animals and plants

(2013) Thorsten B. H. Reusch   Evolutionary Applications

A developmental and energetic basis linking larval oyster shell formation to acidification sensitivity

(2013) George G. Waldbusser et al.   GEOPHYSICAL RESEARCH LETTERS

Natural variation and the capacity to adapt to ocean acidification in the keystone sea urchinStrongylocentrotus purpuratus

(2013) Morgan W. Kelly et al.   GLOBAL CHANGE BIOLOGY

Effects of sea-water acidification on fertilization and larval development of the oyster Crassostrea gigas

(2013) P. Barros et al.   JOURNAL OF EXPERIMENTAL MARINE BIOLOGY AND ECOLOGY

Impacts of ocean acidification on marine shelled molluscs

(2013) Frédéric Gazeau et al.   MARINE BIOLOGY

Transcriptomic responses to ocean acidification in larval sea urchins from a naturally variable pH environment

(2013) Tyler G. Evans et al.   MOLECULAR ECOLOGY

Adaptation and acclimatization to ocean acidification in marine ectotherms: an in situ transplant experiment with polychaetes at a shallow CO2 vent system

(2013) P. Calosi et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Evolutionary change during experimental ocean acidification

(2013) M. H. Pespeni et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolution in an acidifying ocean

(2013) Jennifer M. Sunday et al.   TRENDS IN ECOLOGY & EVOLUTION

Analyzing Effects of Naturally Occurring Missense Mutations

(2012) Zhe Zhang et al.   Computational and Mathematical Methods in Medicine

Food availability outweighs ocean acidification effects in juvenileMytilus edulis: laboratory and field experiments

(2012) Jörn Thomsen et al.   GLOBAL CHANGE BIOLOGY

Elevated pCO2 causes developmental delay in early larval Pacific oysters, Crassostrea gigas

(2012) Emma Timmins-Schiffman et al.   MARINE BIOLOGY

Impacts of seawater acidification on mantle gene expression patterns of the Baltic Sea blue mussel: implications for shell formation and energy metabolism

(2012) Anne K. Hüning et al.   MARINE BIOLOGY

Characterization of the Pearl Oyster (Pinctada martensii) Mantle Transcriptome Unravels Biomineralization Genes

(2012) Yaohua Shi et al.   MARINE BIOTECHNOLOGY

Whole Transcriptome Analysis of the CoralAcropora milleporaReveals Complex Responses to CO2-driven Acidification during the Initiation of Calcification

(2012) A. MOYA et al.   MOLECULAR ECOLOGY

Transcriptome-wide polymorphisms of red abalone (Haliotis rufescens) reveal patterns of gene flow and local adaptation

(2012) Pierre De Wit et al.   MOLECULAR ECOLOGY

Population genomics of Pacific lamprey: adaptive variation in a highly dispersive species

(2012) Jon E. Hess et al.   MOLECULAR ECOLOGY

The oyster genome reveals stress adaptation and complexity of shell formation

(2012) Guofan Zhang et al.   NATURE

The transient receptor potential channel TRPA1: from gene to pathophysiology

(2012) Bernd Nilius et al.   PFLUGERS ARCHIV-EUROPEAN JOURNAL OF PHYSIOLOGY

Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species

(2012) Brant K. Peterson et al.   PLoS One

Predicting the Functional Effect of Amino Acid Substitutions and Indels

(2012) Yongwook Choi et al.   PLoS One

Different secretory repertoires control the biomineralization processes of prism and nacre deposition of the pearl oyster shell

(2012) B. Marie et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Early development and molecular plasticity in the Mediterranean sea urchin Paracentrotus lividus exposed to CO2-driven acidification

(2011) S. Martin et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

Proteomic response to elevated PCO2 level in eastern oysters, Crassostrea virginica: evidence for oxidative stress

(2011) L. Tomanek et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

Disk abalone (Haliotis discus discus) expresses a novel antistasin-like serine protease inhibitor: Molecular cloning and immune response against bacterial infection

(2010) Chamilani Nikapitiya et al.   FISH & SHELLFISH IMMUNOLOGY

Carbonate constants for estuarine waters

(2010) Frank J. Millero   MARINE AND FRESHWATER RESEARCH

Populations of the Sydney rock oyster, Saccostrea glomerata, vary in response to ocean acidification

(2010) L. M. Parker et al.   MARINE BIOLOGY

Effects of ocean acidification and high temperatures on the bryozoanMyriapora truncataat natural CO2vents

(2010) Riccardo Rodolfo-Metalpa et al.   Marine Ecology-An Evolutionary Perspective

Elevated level of carbon dioxide affects metabolism and shell formation in oysters Crassostrea virginica (Gmelin)

(2010) E Beniash et al.   MARINE ECOLOGY PROGRESS SERIES

Differential modes of selection on the rhodopsin gene in coastal Baltic and North Sea populations of the sand goby, Pomatoschistus minutus

(2010) MAARTEN H. D. LARMUSEAU et al.   MOLECULAR ECOLOGY

Effects of past, present, and future ocean carbon dioxide concentrations on the growth and survival of larval shellfish

(2010) S. C. Talmage et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Transcriptomic response of sea urchin larvae Strongylocentrotus purpuratus to CO2-driven seawater acidification

(2009) A. E. Todgham et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

Ocean acidification alters skeletogenesis and gene expression in larval sea urchins

(2009) MJ O’Donnell et al.   MARINE ECOLOGY PROGRESS SERIES

Effects of ocean acidification on the immune response of the blue mussel Mytilus edulis

(2008) R Bibby et al.   Aquatic Biology

Undertaker, a Drosophila Junctophilin, Links Draper-Mediated Phagocytosis and Calcium Homeostasis

(2008) Leigh Cuttell et al.   CELL

A Genome-Scan Method to Identify Selected Loci Appropriate for Both Dominant and Codominant Markers: A Bayesian Perspective

(2008) M. Foll et al.   GENETICS

Recombinant perlucin nucleates the growth of calcium carbonate crystals: Molecular cloning and characterization of perlucin from disk abalone, Haliotis discus discus

(2007) Ning Wang et al.   COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY B-BIOCHEMISTRY & MOLECULAR BIOLOGY

Adaptation from standing genetic variation

(2007) R BARRETT et al.   TRENDS IN ECOLOGY & EVOLUTION