Genome of the estuarine oyster provides insights into climate impact and adaptive plasticity

The hard clam genome reveals massive expansion and diversification of inhibitors of apoptosis in Bivalvia

(2021) Hao Song et al.   BMC BIOLOGY

Climatic selection and gene expression plasticity

(2021) Tegan Armarego-Marriott   Nature Climate Change

Construction of a chromosome‐level genome and variation map for the Pacific oyster Crassostrea gigas

(2021) Haigang Qi et al.   Molecular Ecology Resources

A chromosome-level genome assembly for the Pacific oyster Crassostrea gigas

(2021) Carolina Peñaloza et al.   GigaScience

The genome of Nautilus pompilius illuminates eye evolution and biomineralization

(2021) Yang Zhang et al.   Nature Ecology & Evolution

Noncoding Variation and Transcriptional Plasticity Promote Thermal Adaptation in Oysters by Altering Energy Metabolism

(2021) Ao Li et al.   MOLECULAR BIOLOGY AND EVOLUTION

Chromosome-level analysis of the Crassostrea hongkongensis genome reveals extensive duplication of immune-related genes in bivalves

(2020) Jinxia Peng et al.   Molecular Ecology Resources

Adaptation of plasticity to projected maximum temperatures and across climatically defined bioregions

(2020) Jonathan Sandoval-Castillo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolutionary origins of genomic adaptations in an invasive copepod

(2020) David Ben Stern et al.   Nature Ecology & Evolution

The iron-responsive genome of the chiton Acanthopleura Granulata

(2020) Rebecca M Varney et al.   Genome Biology and Evolution

Symbiotic organs shaped by distinct modes of genome evolution in cephalopods

(2019) Mahdi Belcaid et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Adaptation to climate change through genetic accommodation and assimilation of plastic phenotypes

(2019) Morgan Kelly   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Evolutionary trade-offs between baseline and plastic gene expression in two congeneric oyster species

(2019) Ao Li et al.   Biology Letters

Transcriptome and Gene Coexpression Network Analyses of Two Wild Populations Provides Insight into the High-Salinity Adaptation Mechanisms of Crassostrea ariakensis

(2019) A. Xingyu Liu et al.   MARINE BIOTECHNOLOGY

Chromosomal-level assembly of the blood clam, Scapharca (Anadara) broughtonii, using long sequence reads and Hi-C

(2019) Chang-Ming Bai et al.   GigaScience

Combining RNA-seq data and homology-based gene prediction for plants, animals and fungi

(2018) Jens Keilwagen et al.   BMC BIOINFORMATICS

Analysis of Genome-Wide Differentiation between Native and Introduced Populations of the Cupped Oysters Crassostrea gigas and Crassostrea angulata

(2018) Pierre-Alexandre Gagnaire et al.   Genome Biology and Evolution

Divergence and plasticity shape adaptive potential of the Pacific oyster

(2018) Li Li et al.   Nature Ecology & Evolution

Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies

(2018) Michael J. Roach et al.   BMC BIOINFORMATICS

Diversity and Evolution of Living Oysters

(2018) Ximing Guo et al.   JOURNAL OF SHELLFISH RESEARCH

Fast and accurate de novo genome assembly from long uncorrected reads

(2017) Robert Vaser et al.   GENOME RESEARCH

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

More than meets the eye: The barrier effect of the Yangtze River outflow

(2017) Gang Ni et al.   MOLECULAR ECOLOGY

Temperature, energy metabolism, and adaptive divergence in two oyster subspecies

(2017) Ao Li et al.   Ecology and Evolution

Species-specific responses to ocean acidification should account for local adaptation and adaptive plasticity

(2017) Cristian A. Vargas et al.   Nature Ecology & Evolution

Characterization of cholesterol homeostasis in sphingosine-1-phosphate lyase-deficient fibroblasts reveals a Niemann-Pick disease type C-like phenotype with enhanced lysosomal Ca2+ storage

(2017) Hans Vienken et al.   Scientific Reports

The impact of Yangtze River discharge on the genetic structure of a population of the rock bream,Oplegnathus fasciatus

(2016) Yongshuang Xiao et al.   Marine Biology Research

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

How plasticity, genetic assimilation and cryptic genetic variation may contribute to adaptive radiations

(2016) Ralf F. Schneider et al.   MOLECULAR ECOLOGY

Heatmapper: web-enabled heat mapping for all

(2016) Sasha Babicki et al.   NUCLEIC ACIDS RESEARCH

Infectious diseases of marine molluscs and host responses as revealed by genomic tools

(2016) Ximing Guo et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Molecular Basis for Adaptation of Oysters to Stressful Marine Intertidal Environments

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

The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing

(2016) Alvaro Martinez Barrio et al.   eLife

Four billion people facing severe water scarcity

(2016) M. M. Mekonnen et al.   Science Advances

Gene expression plasticity as a mechanism of coral adaptation to a variable environment

(2016) Carly D. Kenkel et al.   Nature Ecology & Evolution

Immune and stress responses in oysters with insights on adaptation

(2015) Ximing Guo et al.   FISH & SHELLFISH IMMUNOLOGY

Reef-Specific Patterns of Gene Expression Plasticity in Eastern Oysters (Crassostrea virginica)

(2015) Laura E. Eierman et al.   JOURNAL OF HEREDITY

Salinity changes in the World Ocean since 1950 in relation to changing surface freshwater fluxes

(2014) Nikolaos Skliris et al.   CLIMATE DYNAMICS

Mitochondrial DNA sequence analysis from multiple gene fragments reveals genetic heterogeneity of Crassostrea ariakensis in East Asia

(2014) Woo-Jin Kim et al.   Genes & Genomics

PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses in R

(2014) Bastian Pfeifer et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

PASTEC: An Automatic Transposable Element Classification Tool

(2014) Claire Hoede et al.   PLoS One

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Gene expression under chronic heat stress in populations of the mustard hill coral (Porites astreoides ) from different thermal environments

(2013) C. D. Kenkel et al.   MOLECULAR ECOLOGY

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions

(2013) Joshua N Burton et al.   NATURE BIOTECHNOLOGY

Increase in the range between wet and dry season precipitation

(2013) Chia Chou et al.   Nature Geoscience

Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions

(2013) Jaina Mistry et al.   NUCLEIC ACIDS RESEARCH

Adaptive phenotypic plasticity and local adaptation for temperature tolerance in freshwater zooplankton

(2013) L. Y. Yampolsky et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The genomic determinants of genotype × environment interactions in gene expression

(2013) Vladislav Grishkevich et al.   TRENDS IN GENETICS

REAPR: a universal tool for genome assembly evaluation

(2013) Martin Hunt et al.   GENOME BIOLOGY

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

The oyster genome reveals stress adaptation and complexity of shell formation

(2012) Guofan Zhang et al.   NATURE

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity

(2012) Y. Wang et al.   NUCLEIC ACIDS RESEARCH

Phylogeography of Bivalve Cyclina sinensis: Testing the Historical Glaciations and Changjiang River Outflow Hypotheses in Northwestern Pacific

(2012) Gang Ni et al.   PLoS One

Oyster Reefs at Risk and Recommendations for Conservation, Restoration, and Management

(2011) Michael W. Beck et al.   BIOSCIENCE

Classification of a Common Cupped Oyster from Southern China

(2011) Haiyan Wang et al.   JOURNAL OF SHELLFISH RESEARCH

Inference of human population history from individual whole-genome sequences

(2011) Heng Li et al.   NATURE

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Population genetics of Crassostrea ariakensis in Asia inferred from microsatellite markers

(2010) Jie Xiao et al.   MARINE BIOLOGY

The Solute Carrier Families Have a Remarkably Long Evolutionary History with the Majority of the Human Families Present before Divergence of Bilaterian Species

(2010) P. J. Hoglund et al.   MOLECULAR BIOLOGY AND EVOLUTION

CDD: a Conserved Domain Database for the functional annotation of proteins

(2010) A. Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

The Impact of Climate Change on the World's Marine Ecosystems

(2010) O. Hoegh-Guldberg et al.   SCIENCE

Phenotypic plasticity's impacts on diversification and speciation

(2010) David W. Pfennig et al.   TRENDS IN ECOLOGY & EVOLUTION

Insights into the residence in lipid rafts of adenylyl cyclase AC8 and its regulation by capacitative calcium entry

(2009) Mario Pagano et al.   AMERICAN JOURNAL OF PHYSIOLOGY-CELL PHYSIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Fast model-based estimation of ancestry in unrelated individuals

(2009) D. H. Alexander et al.   GENOME RESEARCH

genBlastA: Enabling BLAST to identify homologous gene sequences

(2008) R. She et al.   GENOME RESEARCH

Temperature adaptation of cytosolic malate dehydrogenases of limpets (genus Lottia): differences in stability and function due to minor changes in sequence correlate with biogeographic and vertical distributions

(2008) Y. Dong et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

Classification of Common Oysters from North China

(2008) Haiyan Wang et al.   JOURNAL OF SHELLFISH RESEARCH