Adaptive divergence and underlying mechanisms in response to salinity gradients between two Crassostrea oysters revealed by phenotypic and transcriptomic analyses

Comparative Genomics Reveals Evolutionary Drivers of Sessile Life and Left-right Shell Asymmetry in Bivalves

(2022) Yang Zhang et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Local environment‐driven adaptive evolution in a marine invasive ascidian ( Molgula manhattensis )

(2021) Yiyong Chen et al.   Ecology and Evolution

Comparative study on the growth, survival, gonad development and trait segregation of F2 hybrids and their grandparent species (Crassostrea ariakensis and C. hongkongensis)

(2021) Yanping Qin et al.   AQUACULTURE

Chromosome‐level genome and population genomic analysis provide insights into the evolution and environmental adaptation of Jinjiang oyster Crassostrea ariakensis

(2021) Biao Wu et al.   Molecular Ecology Resources

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

(2021) Ao Li et al.   Communications Biology

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

(2020) Bui Quang Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Insights into the strategy of micro-environmental adaptation: Transcriptomic analysis of two alvinocaridid shrimps at a hydrothermal vent

(2020) Fang-Chao Zhu et al.   PLoS One

A comparative analysis of the growth, survival and reproduction of Crassostrea hongkongensis, Crassostrea ariakensis, and their diploid and triploid hybrids

(2020) Yanping Qin et al.   AQUACULTURE

Species-specific molecular responses of wild coral reef fishes during a marine heatwave

(2020) Moisés A. Bernal et al.   Science Advances

Identification of differentially expressed genes in gills of tiger puffer (Takifugu rubripes) in response to low-salinity stress

(2020) Jie-Lan Jiang et al.   COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY B-BIOCHEMISTRY & MOLECULAR BIOLOGY

Metabolic contribution to salinity stress response in grains of two barley cultivars with contrasting salt tolerance

(2020) Zaynab Derakhshani et al.   ENVIRONMENTAL AND EXPERIMENTAL BOTANY

Improved estimates of changes in upper ocean salinity and the hydrological cycle

(2020) Lijing Cheng et al.   JOURNAL OF CLIMATE

Novel insights into the genetic diversity and clonal structure of natural trembling aspen ( Populus tremuloides Michx.) populations: A transcontinental study

(2019) Mathieu Latutrie et al.   JOURNAL OF BIOGEOGRAPHY

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

Multifaceted regulation of the system A transporter Slc38a2 suggests nanoscale regulation of amino acid metabolism and cellular signaling

(2019) Robin Johansen Menchini et al.   NEUROPHARMACOLOGY

Thermotolerance Divergence Revealed by the Physiological and Molecular Responses in Two Oyster Subspecies of Crassostrea gigas in China

(2019) Hamze Ghaffari et al.   Frontiers in Physiology

Comparative genomics reveals divergent thermal selection in warm‐ and cold‐tolerant marine mussels

(2019) Iva Popovic et al.   MOLECULAR ECOLOGY

Population genomics of finless porpoises reveal an incipient cetacean species adapted to freshwater

(2018) Xuming Zhou et al.   Nature Communications

Strong phenotypic plasticity limits potential for evolutionary responses to climate change

(2018) Vicencio Oostra et al.   Nature Communications

Divergence and plasticity shape adaptive potential of the Pacific oyster

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

Parallel transcriptome evolution in stream threespine sticklebacks

(2018) Jun Kitano et al.   DEVELOPMENT GROWTH & DIFFERENTIATION

Analysis of in situ Transcriptomes Reveals Divergent Adaptive Response to Hyper- and Hypo-Salinity in the Hong Kong Oyster, Crassostrea hongkongensis

(2018) Shu Xiao et al.   Frontiers in Physiology

Phenotypic plasticity in gene expression and physiological response in red drum Sciaenops ocellatus exposed to a long-term freshwater environment

(2017) Mariel Gullian Klanian et al.   FISH PHYSIOLOGY AND BIOCHEMISTRY

In situ common garden assays demonstrate increased defense against natural fouling in non-native populations of the red seaweed Gracilaria vermiculophylla

(2017) Shasha Wang et al.   MARINE BIOLOGY

Convergent Evolution of the Osmoregulation System in Decapod Shrimps

(2017) Jianbo Yuan et al.   MARINE BIOTECHNOLOGY

Transcriptomic responses to seawater acidification among sea urchin populations inhabiting a natural pH mosaic

(2017) Tyler G. Evans et al.   MOLECULAR ECOLOGY

Transcriptomic analysis of Crassostrea sikamea × Crassostrea angulata hybrids in response to low salinity stress

(2017) Lulu Yan et al.   PLoS One

Adaptive and non-adaptive divergence in a common landscape

(2017) Joost A. M. Raeymaekers et al.   Nature Communications

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

(2017) Ao Li et al.   Ecology and Evolution

LPEseq: Local-Pooled-Error Test for RNA Sequencing Experiments with a Small Number of Replicates

(2016) Jungsoo Gim et al.   PLoS One

Mechanisms of Cl− uptake in rainbow trout: Cloning and expression of slc26a6, a prospective Cl−/HCO3− exchanger

(2015) David Boyle et al.   COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY A-MOLECULAR & INTEGRATIVE PHYSIOLOGY

The environmental genomics of metazoan thermal adaptation

(2015) D Porcelli et al.   HEREDITY

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

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

The red coral (Corallium rubrum ) transcriptome: a new resource for population genetics and local adaptation studies

(2015) M. Pratlong et al.   Molecular Ecology Resources

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Hybrid zones: windows on climate change

(2015) Scott A. Taylor et al.   TRENDS IN ECOLOGY & EVOLUTION

jvenn: an interactive Venn diagram viewer

(2014) Philippe Bardou et al.   BMC BIOINFORMATICS

Transcriptome Changes in Eriocheir sinensis Megalopae after Desalination Provide Insights into Osmoregulation and Stress Adaption in Larvae

(2014) Min Hui et al.   PLoS One

Concentrations, Accumulation, and Interactions of Redoximorphic Metals (Fe, Mn) Between Other Elements in Plants Grown on Wastewater-Irrigated and Control Soils

(2014) Halim Avci et al.   WATER AIR AND SOIL POLLUTION

Increase in the range between wet and dry season precipitation

(2013) Chia Chou et al.   Nature Geoscience

Genome and Transcriptome Analyses Provide Insight into the Euryhaline Adaptation Mechanism of Crassostrea gigas

(2013) Jie Meng et al.   PLoS One

SLC4 family transporters in a marine diatom directly pump bicarbonate from seawater

(2013) K. Nakajima et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolution of growth by genetic accommodation in Icelandic freshwater stickleback

(2013) B. W. Robinson   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

(2012) Pablo Cingolani et al.   FLY

Energy homeostasis as an integrative tool for assessing limits of environmental stress tolerance in aquatic invertebrates

(2012) Inna M. Sokolova et al.   MARINE ENVIRONMENTAL RESEARCH

The genomic basis of adaptive evolution in threespine sticklebacks

(2012) Felicity C. Jones et al.   NATURE

Unusual conservation of mitochondrial gene order in Crassostrea oysters: evidence for recent speciation in Asia

(2011) Jianfeng Ren et al.   BMC EVOLUTIONARY BIOLOGY

Complete mitochondrial DNA sequence of Crassostrea nippona: comparative and phylogenomic studies on seven commercial Crassostrea species

(2011) Hong Yu et al.   MOLECULAR BIOLOGY REPORTS

Local Adaptation in Marine Invertebrates

(2010) Eric Sanford et al.   Annual Review of Marine Science

Response of Mytilus galloprovincialis (L.) to increasing seawater temperature and to marteliosis: Metabolic and physiological parameters

(2010) Andreas Anestis et al.   COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY A-MOLECULAR & INTEGRATIVE PHYSIOLOGY

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

(2010) A. McKenna et al.   GENOME RESEARCH

Detecting population structure in a high gene-flow species, Atlantic herring (Clupea harengus): direct, simultaneous evaluation of neutral vs putatively selected loci

(2010) C André et al.   HEREDITY

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

Gene ontology analysis for RNA-seq: accounting for selection bias

(2010) Matthew D Young et al.   GENOME BIOLOGY

Divergence in host use ability of a marine herbivore from two habitat types

(2009) O. VESAKOSKI et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Identification of intestinal bicarbonate transporters involved in formation of carbonate precipitates to stimulate water absorption in marine teleost fish

(2008) Yukihiro Kurita et al.   AMERICAN JOURNAL OF PHYSIOLOGY-REGULATORY INTEGRATIVE AND COMPARATIVE PHYSIOLOGY

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

FINE-SCALE ADAPTATION IN A CLONAL SEA ANEMONE

(2008) Craig D. H. Sherman et al.   EVOLUTION

Fine-Scale Population Genetic Structure of Zhikong Scallop (Chlamys farreri): Do Local Marine Currents Drive Geographical Differentiation?

(2008) Aibin Zhan et al.   MARINE BIOTECHNOLOGY