4.6 Article

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

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Biochemistry & Molecular Biology

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

Caroline Schwaner et al.

Summary: Calcifying marine organisms, such as the eastern oyster, are vulnerable to ocean acidification. This study found that the perlucin gene plays a protective role in mitigating the effects of ocean acidification.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2023)

Article Ecology

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

Kara K. S. Layton et al.

Summary: The study proposes a broadening of genetic variant research to include structural and epigenetic variants that play important roles in adaptation, in order to improve the prediction power of species response to climate change, especially for weakly structured or panmictic species. This can help reveal the molecular mechanisms underlying species' response to climate change.

JOURNAL OF ANIMAL ECOLOGY (2022)

Article Biochemical Research Methods

Analysing high-throughput sequencing data in Python with HTSeq 2.0

Givanna H. Putri et al.

Summary: HTSeq 2.0 provides an expanded application programming interface, including a new representation for sparse genomic data, enhancements for htseq-count to accommodate single-cell omics, a new script for data using cell and molecular barcodes, improved documentation, testing and deployment, bug fixes, and Python 3 support.

BIOINFORMATICS (2022)

Article Evolutionary Biology

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

Isabelle Boutet et al.

Summary: This study presents a chromosome-level assembly and annotation of the European flat oyster genome using a combination of PacBio, Illumina, 10X linked, and Hi-C sequencing. The assembled genome has a size of 887.2 Mb with a scaffold-N50 of 97.1 Mb, scaffolded on 10 pseudochromosomes. Annotation of the genome identified 35,962 protein-coding genes. The study also provides insights into transposable element diversity, tRNA and miRNA composition, and the molecular response of O. edulis to the parasite M. refringens. This genome assembly serves as a valuable resource for further genomic studies and genetic breeding in support of oyster aquaculture and natural reef restoration.

EVOLUTIONARY APPLICATIONS (2022)

Article Genetics & Heredity

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

Michelle Barbosa et al.

Summary: The study revealed that the eastern oyster demonstrates significant recovery and acclimation when adapting to ocean acidification, supported by transcriptomic analysis. The functions of differentially expressed genes include cell differentiation, development, biomineralization, ion exchange, and immunity. The findings suggest acclimation as a mode of resilience to ocean acidification.
Article Ecology

Magnitude and Predictability of pH Fluctuations Shape Plastic Responses to Ocean Acidification

Mark C. Bitter et al.

Summary: The study demonstrates that different habitats' environmental fluctuations have an impact on the plasticity of gene expression in mussels, showing population differences. Mussels native to habitats with large pH fluctuations and low predictability display reduced phenotypic plasticity in experimental treatments.

AMERICAN NATURALIST (2021)

Article Environmental Sciences

Acidification stress effect on umbonate veliger larval development in Panopea globosa

Edgar A. Lopez-Landavery et al.

Summary: Ocean acidification affects the development of Panopea globosa umbonate veliger larvae, causing reduced growth, shell damage, and increased energy expenditure for maintaining homeostasis.

MARINE POLLUTION BULLETIN (2021)

Article Biochemistry & Molecular Biology

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

Menno J. de Jong et al.

Summary: SambaR is an integrative and user-friendly R package designed to automate and simplify quality control and population-genetic analyses of biallelic SNP data sets. Users can perform mainstream population-genetic analyses with fewer than 10 commands and generate a wide variety of ready-to-publish graphs.

MOLECULAR ECOLOGY RESOURCES (2021)

Article Biodiversity Conservation

Oyster biomineralization under ocean acidification: From genes to shell

Kanmani Chandra Rajan et al.

Summary: The study suggests that mantle tissue in oysters can maintain biomineralization under ocean acidification conditions, with normal shell growth and mechanical properties. Ocean acidification is more of a 'dissolution problem' rather than a 'biomineralization problem' for resilient species.

GLOBAL CHANGE BIOLOGY (2021)

Article Environmental Sciences

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

Kanmani Chandra Rajan et al.

MARINE ENVIRONMENTAL RESEARCH (2020)

Article Marine & Freshwater Biology

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

Grace K. Saba et al.

ESTUARINE COASTAL AND SHELF SCIENCE (2019)

Article Biochemistry & Molecular Biology

Stacks 2: Analytical methods for paired-end sequencing improve RADseq-based population genomics

Nicolas C. Rochette et al.

MOLECULAR ECOLOGY (2019)

Article Biotechnology & Applied Microbiology

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

Daehwan Kim et al.

NATURE BIOTECHNOLOGY (2019)

Article Evolutionary Biology

Insights into the Evolution of Shells and Love Darts of Land Snails Revealed from Their Matrix Proteins

Keisuke Shimizu et al.

GENOME BIOLOGY AND EVOLUTION (2019)

Article Biochemistry & Molecular Biology

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

Valentin Foulon et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2019)

Article Multidisciplinary Sciences

Standing genetic variation fuels rapid adaptation to ocean acidification

M. C. Bitter et al.

NATURE COMMUNICATIONS (2019)

Article Genetics & Heredity

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

Zeynep Coban-Akdemir et al.

AMERICAN JOURNAL OF HUMAN GENETICS (2018)

Article Biochemistry & Molecular Biology

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

L. T. Sigle et al.

INSECT MOLECULAR BIOLOGY (2018)

Article Marine & Freshwater Biology

Transcriptomic analysis of embryo development in the invasive snail Pomacea canaliculata

Yaming Xiong et al.

JOURNAL OF MOLLUSCAN STUDIES (2018)

Article Biology

Ocean pH fluctuations affect mussel larvae at key developmental transitions

L. Kapsenberg et al.

PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2018)

Article Fisheries

Metabolic cost of calcification in bivalve larvae under experimental ocean acidification

Christina A. Frieder et al.

ICES JOURNAL OF MARINE SCIENCE (2017)

Article Biochemistry & Molecular Biology

Insights from the Shell Proteome: Biomineralization to Adaptation

Jaison Arivalagan et al.

MOLECULAR BIOLOGY AND EVOLUTION (2017)

Article Biochemistry & Molecular Biology

pcadapt: an R package to perform genome scans for selection based on principal component analysis

Keurcien Luu et al.

MOLECULAR ECOLOGY RESOURCES (2017)

Review Fisheries

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

Mario Alberto Burgos-Aceves et al.

FISH & SHELLFISH IMMUNOLOGY (2017)

Article Biochemistry & Molecular Biology

Transcriptomic profiling of adaptive responses to ocean acidification

Priscila Goncalves et al.

MOLECULAR ECOLOGY (2017)

Article Multidisciplinary Sciences

Naturally acidified habitat selects for ocean acidification-tolerant mussels

Joern Thomsen et al.

SCIENCE ADVANCES (2017)

Article Biotechnology & Applied Microbiology

Transcriptomic response of the Antarctic pteropod Limacina helicina antarctica to ocean acidification

Kevin M. Johnson et al.

BMC GENOMICS (2017)

Article Biochemistry & Molecular Biology

Functional analysis of a tyrosinase gene involved in early larval shell biogenesis in Crassostrea angulata and its response to ocean acidification

Bingye Yang et al.

COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY B-BIOCHEMISTRY & MOLECULAR BIOLOGY (2017)

Article Environmental Sciences

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

Janine Waege et al.

ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY (2016)

Article Biochemistry & Molecular Biology

Rapid transcriptional acclimation following transgenerational exposure of oysters to ocean acidification

Priscila Goncalves et al.

MOLECULAR ECOLOGY (2016)

Review Agriculture, Dairy & Animal Science

Molecular Basis for Adaptation of Oysters to Stressful Marine Intertidal Environments

Guofan Zhang et al.

ANNUAL REVIEW OF ANIMAL BIOSCIENCES, VOL 4 (2016)

Article Multidisciplinary Sciences

Experimental ocean acidification alters the allocation of metabolic energy

T. -C. Francis Pan et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)

Review Geochemistry & Geophysics

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

George G. Waldbusser et al.

ANNUAL REVIEW OF MARINE SCIENCE, VOL 6 (2014)

Article Biotechnology & Applied Microbiology

Shotgun proteomics reveals physiological response to ocean acidification in Crassostrea gigas

Emma Timmins-Schiffman et al.

BMC GENOMICS (2014)

Article Biochemistry & Molecular Biology

Multilocus Adaptation Associated with Heat Resistance in Reef-Building Corals

Rachael A. Bay et al.

CURRENT BIOLOGY (2014)

Article Marine & Freshwater Biology

Coastal ocean acidification: The other eutrophication problem

Ryan B. Wallace et al.

ESTUARINE COASTAL AND SHELF SCIENCE (2014)

Review Ecology

Evolution in an acidifying ocean

Jennifer M. Sunday et al.

TRENDS IN ECOLOGY & EVOLUTION (2014)

Article Environmental Sciences

Adaptation of a globally important coccolithophore to ocean warming and acidification

Lothar Schlueter et al.

NATURE CLIMATE CHANGE (2014)

Review Zoology

Mollusk shell structures and their formation mechanism

Michio Suzuki et al.

CANADIAN JOURNAL OF ZOOLOGY-REVUE CANADIENNE DE ZOOLOGIE (2013)

Article Geosciences, Multidisciplinary

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

George G. Waldbusser et al.

GEOPHYSICAL RESEARCH LETTERS (2013)

Article Ecology

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

P. Barros et al.

JOURNAL OF EXPERIMENTAL MARINE BIOLOGY AND ECOLOGY (2013)

Article Biochemistry & Molecular Biology

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

Jon E. Hess et al.

MOLECULAR ECOLOGY (2013)

Review Biochemistry & Molecular Biology

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

Tyler G. Evans et al.

MOLECULAR ECOLOGY (2013)

Article Marine & Freshwater Biology

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

Emma Timmins-Schiffman et al.

MARINE BIOLOGY (2013)

Article Marine & Freshwater Biology

Impacts of ocean acidification on marine shelled molluscs

Frederic Gazeau et al.

MARINE BIOLOGY (2013)

Article Biotechnology & Applied Microbiology

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

Yaohua Shi et al.

MARINE BIOTECHNOLOGY (2013)

Article Multidisciplinary Sciences

Evolutionary change during experimental ocean acidification

Melissa H. Pespeni et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)

Review Mathematical & Computational Biology

Analyzing Effects of Naturally Occurring Missense Mutations

Zhe Zhang et al.

COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE (2012)

Article Multidisciplinary Sciences

The oyster genome reveals stress adaptation and complexity of shell formation

Guofan Zhang et al.

NATURE (2012)

Article Multidisciplinary Sciences

Predicting the Functional Effect of Amino Acid Substitutions and Indels

Yongwook Choi et al.

PLOS ONE (2012)

Review Physiology

The transient receptor potential channel TRPA1: from gene to pathophysiology

Bernd Nilius et al.

PFLUGERS ARCHIV-EUROPEAN JOURNAL OF PHYSIOLOGY (2012)

Article Multidisciplinary Sciences

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

Benjamin Marie et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)

Article Biochemical Research Methods

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

Mark D. Robinson et al.

BIOINFORMATICS (2010)

Article Fisheries

Carbonate constants for estuarine waters

Frank J. Millero

MARINE AND FRESHWATER RESEARCH (2010)

Article Marine & Freshwater Biology

Effects of ocean acidification and high temperatures on the bryozoan Myriapora truncata at natural CO2 vents

Riccardo Rodolfo-Metalpa et al.

MARINE ECOLOGY-AN EVOLUTIONARY PERSPECTIVE (2010)

Article Ecology

Ocean acidification alters skeletogenesis and gene expression in larval sea urchins

Michael J. O'Donnell et al.

MARINE ECOLOGY PROGRESS SERIES (2010)

Article Multidisciplinary Sciences

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

Stephanie C. Talmage et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)

Article Marine & Freshwater Biology

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

Ruth Bibby et al.

AQUATIC BIOLOGY (2008)

Article Biochemistry & Molecular Biology

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

Ning Wang et al.

COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY B-BIOCHEMISTRY & MOLECULAR BIOLOGY (2008)

Review Ecology

Adaptation from standing genetic variation

Rowan D. H. Barrett et al.

TRENDS IN ECOLOGY & EVOLUTION (2008)

Article Geosciences, Multidisciplinary

Impact of elevated CO2 on shellfish calcification

Frederic Gazeau et al.

GEOPHYSICAL RESEARCH LETTERS (2007)

Article Biochemistry & Molecular Biology

Trivalent recognition unit of innate immunity system - Crystal structure of trimeric human M-ficolin fibrinogen-like domain

Michikazu Tanio et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2007)

Article Biochemistry & Molecular Biology

Tyrosinase localization in mollusc shells

Kouhei Nagai et al.

COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY B-BIOCHEMISTRY & MOLECULAR BIOLOGY (2007)

Article Immunology

Role of ficolin in innate immunity and its molecular basis

Yuichi Endo et al.

IMMUNOBIOLOGY (2007)

Article Multidisciplinary Sciences

Hemocyte-mediated shell mineralization in the eastern oyster

AS Mount et al.

SCIENCE (2004)

Article Biochemistry & Molecular Biology

Draper-mediated and phosphatidylserine-independent phagocytosis of apoptotic cells by drosophila hemocytes/macrophages

J Manaka et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2004)

Article Microscopy

The nacre protein perlucin nucleates growth of calcium carbonate crystals

S Blank et al.

JOURNAL OF MICROSCOPY-OXFORD (2003)