Divergence, evolution and adaptation in ray-finned fish genomes

Imprecise naming: the anadromous and the sea spawning threespine stickleback should be discriminated by names

(2018) Harald Ahnelt   BIOLOGIA

De novo transcriptome assembly, annotation and comparison of four ecological and evolutionary model salmonid fish species

(2018) Madeleine Carruthers et al.   BMC GENOMICS

Transcriptome Analysis Based on RNA-Seq in Understanding Pathogenic Mechanisms of Diseases and the Immune System of Fish: A Comprehensive Review

(2018) Arun Sudhagar et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data

(2018) Lily C. Hughes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Resolving the ray-finned fish tree of life

(2018) Michael E. Alfaro   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A genome-wide association study on growth traits in orangespotted grouper (Epinephelus coioides) with RAD-seq genotyping

(2018) Hui Yu et al.   Science China-Life Sciences

An epigenetic regulatory switch controlling temperature-dependent sex determination in vertebrates

(2018) Xi-Yin Li et al.   Science China-Life Sciences

Draft genome of the protandrous Chinese black porgy, Acanthopagrus schlegelii

(2018) Zhiyong Zhang et al.   GigaScience

Mudskippers and Their Genetic Adaptations to an Amphibious Lifestyle

(2018) Xinxin You et al.   Animals

High resolution annotation of zebrafish transcriptome using long-read sequencing

(2018) German Nudelman et al.   GENOME RESEARCH

Diverse and variable sex determination mechanisms in vertebrates

(2018) Xi-Yin Li et al.   Science China-Life Sciences

Whole-Genome Sequencing of Chinese Yellow Catfish Provides a Valuable Genetic Resource for High-Throughput Identification of Toxin Genes

(2018) Shiyong Zhang et al.   Toxins

Single-cell transcriptome analysis of fish immune cells provides insight into the evolution of vertebrate immune cell types

(2017) Santiago J. Carmona et al.   GENOME RESEARCH

High-Throughput Identification of Antimicrobial Peptides from Amphibious Mudskippers

(2017) Yunhai Yi et al.   Marine Drugs

China is initiating the Aquatic 10-100-1,000 Genomics Program

(2017) Yingjie Liu et al.   Science China-Life Sciences

Genomic Selection in Plant Breeding: Methods, Models, and Perspectives

(2017) José Crossa et al.   TRENDS IN PLANT SCIENCE

Nanopore long-read RNAseq reveals widespread transcriptional variation among the surface receptors of individual B cells

(2017) Ashley Byrne et al.   Nature Communications

The rises and falls of opsin genes in 59 ray-finned fish genomes and their implications for environmental adaptation

(2017) Jinn-Jy Lin et al.   Scientific Reports

Gene editing nuclease and its application in tilapia

(2017) Minghui Li et al.   Science Bulletin

Comparative Transcriptomic Study of Muscle Provides New Insights into the Growth Superiority of a Novel Grouper Hybrid

(2017) Ying Sun et al.   PLoS One

The Sinocyclocheilus cavefish genome provides insights into cave adaptation

(2016) Junxing Yang et al.   BMC BIOLOGY

Transcriptome analysis reveals the molecular mechanisms underlying growth superiority in a novel grouper hybrid (Epinephelus fuscogutatus♀ × E. lanceolatus♂)

(2016) Ying Sun et al.   BMC GENETICS

Transcriptome wide analyses reveal a sustained cellular stress response in the gill tissue of Trematomus bernacchii after acclimation to multiple stressors

(2016) Troy J. Huth et al.   BMC GENOMICS

The Genome of the Self-Fertilizing Mangrove Rivulus Fish,Kryptolebias marmoratus: A Model for Studying Phenotypic Plasticity and Adaptations to Extreme Environments

(2016) Joanna L. Kelley et al.   Genome Biology and Evolution

Genomic Basis of Adaptive Evolution: The Survival of Amur Ide (Leuciscuswaleckii) in an Extremely Alkaline Environment

(2016) Jian Xu et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Atlantic salmon genome provides insights into rediploidization

(2016) Sigbjørn Lien et al.   NATURE

The seahorse genome and the evolution of its specialized morphology

(2016) Qiang Lin et al.   NATURE

Three decades of nanopore sequencing

(2016) David Deamer et al.   NATURE BIOTECHNOLOGY

Erratum: Corrigendum: The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons

(2016) Ingo Braasch et al.   NATURE GENETICS

The genome and transcriptome of Japanese flounder provide insights into flatfish asymmetry

(2016) Changwei Shao et al.   NATURE GENETICS

The channel catfish genome sequence provides insights into the evolution of scale formation in teleosts

(2016) Zhanjiang Liu et al.   Nature Communications

Genetic basis of hindlimb loss in a naturally occurring vertebrate model

(2016) Emily K. Don et al.   Biology Open

The genome of the largest bony fish, ocean sunfish (Mola mola), provides insights into its fast growth rate

(2016) Hailin Pan et al.   GigaScience

High-quality genome assembly of channel catfish, Ictalurus punctatus

(2016) Xiaohui Chen et al.   GigaScience

Fish-T1K (Transcriptomes of 1,000 Fishes) Project: large-scale transcriptome data for fish evolution studies

(2016) Ying Sun et al.   GigaScience

A chromosome-level genome assembly of the Asian arowana, Scleropages formosus

(2016) Jia Li et al.   Scientific Data

The genome of the miiuy croaker reveals well-developed innate immune and sensory systems

(2016) Tianjun Xu et al.   Scientific Reports

The Asian arowana (Scleropages formosus) genome provides new insights into the evolution of an early lineage of teleosts

(2016) Chao Bian et al.   Scientific Reports

Whole-genome shotgun sequence assembly enables rapid gene characterization in the tropical fish barramundi,Lates calcarifer

(2015) Jose A. Domingos et al.   ANIMAL GENETICS

A novel sex-determining QTL in Nile tilapia (Oreochromis niloticus)

(2015) Christos Palaiokostas et al.   BMC GENOMICS

A Platform for Rapid Exploration of Aging and Diseases in a Naturally Short-Lived Vertebrate

(2015) Itamar Harel et al.   CELL

Whole Genome Sequencing of the Asian Arowana (Scleropages formosus) Provides Insights into the Evolution of Ray-Finned Fishes

(2015) Christopher M. Austin et al.   Genome Biology and Evolution

Molecular Evolution of Aralkylamine N-Acetyltransferase in Fish: A Genomic Survey

(2015) Jia Li et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Population genomics of natural and experimental populations of guppies (Poecilia reticulata)

(2015) Bonnie A. Fraser et al.   MOLECULAR ECOLOGY

Genomic Resources Notes Accepted 1 June 2015 - 31 July 2015

(2015) et al.   Molecular Ecology Resources

The draft genome of the grass carp (Ctenopharyngodon idellus) provides insights into its evolution and vegetarian adaptation

(2015) Yaping Wang et al.   NATURE GENETICS

Genetic basis and biotechnological manipulation of sexual dimorphism and sex determination in fish

(2015) Jie Mei et al.   Science China-Life Sciences

Signatures of selection in tilapia revealed by whole genome resequencing

(2015) Jun Hong Xia et al.   Scientific Reports

Comprehensive Transcriptome Analysis of Six Catfish Species from an Altitude Gradient Reveals Adaptive Evolution in Tibetan Fishes

(2015) Xiuhui Ma et al.   G3-Genes Genomes Genetics

A Tandem Duplicate of Anti-Müllerian Hormone with a Missense SNP on the Y Chromosome Is Essential for Male Sex Determination in Nile Tilapia, Oreochromis niloticus

(2015) Minghui Li et al.   PLoS Genetics

Genome Sequencing of the Perciform Fish Larimichthys crocea Provides Insights into Molecular and Genetic Mechanisms of Stress Adaptation

(2015) Jingqun Ao et al.   PLoS Genetics

Bioactive Components in Fish Venoms

(2015) Rebekah Ziegman et al.   Toxins

PacBio Sequencing and Its Applications

(2015) Anthony Rhoads et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Genetic variation at aryl hydrocarbon receptor (AHR) loci in populations of Atlantic killifish (Fundulus heteroclitus) inhabiting polluted and reference habitats

(2014) Adam M Reitzel et al.   BMC EVOLUTIONARY BIOLOGY

Analysis of hypoxia-inducible factor alpha polyploidization reveals adaptation to Tibetan plateau in the evolution of schizothoracine fish

(2014) Lihong Guan et al.   BMC EVOLUTIONARY BIOLOGY

Sequencing and characterization of the transcriptome of half-smooth tongue sole (Cynoglossus semilaevis)

(2014) Wenji Wang et al.   BMC GENOMICS

A Tarantula-Venom Peptide Antagonizes the TRPA1 Nociceptor Ion Channel by Binding to the S1–S4 Gating Domain

(2014) Junhong Gui et al.   CURRENT BIOLOGY

Transcription factors involved in retinogenesis are co-opted by the circadian clock following photoreceptor differentiation

(2014) R. Laranjeiro et al.   DEVELOPMENT

Stress response or beneficial temperature acclimation: transcriptomic signatures in Antarctic fish (Pachycara brachycephalum)

(2014) H. S. Windisch et al.   MOLECULAR ECOLOGY

Whole-genome duplication in teleost fishes and its evolutionary consequences

(2014) Stella M. K. Glasauer et al.   MOLECULAR GENETICS AND GENOMICS

The genomic substrate for adaptive radiation in African cichlid fish

(2014) David Brawand et al.   NATURE

Genome sequence and genetic diversity of the common carp, Cyprinus carpio

(2014) Peng Xu et al.   NATURE GENETICS

Whole-genome sequence of a flatfish provides insights into ZW sex chromosome evolution and adaptation to a benthic lifestyle

(2014) Songlin Chen et al.   NATURE GENETICS

Full-length RNA-seq from single cells using Smart-seq2

(2014) Simone Picelli et al.   Nature Protocols

The Genome and Linkage Map of the Northern Pike (Esox lucius): Conserved Synteny Revealed between the Salmonid Sister Group and the Neoteleostei

(2014) Eric B. Rondeau et al.   PLoS One

Mudskipper genomes provide insights into the terrestrial adaptation of amphibious fishes

(2014) Xinxin You et al.   Nature Communications

Co-option of Sox3 as the male-determining factor on the Y chromosome in the fish Oryzias dancena

(2014) Yusuke Takehana et al.   Nature Communications

The draft genome of the large yellow croaker reveals well-developed innate immunity

(2014) Changwen Wu et al.   Nature Communications

The cavefish genome reveals candidate genes for eye loss

(2014) Suzanne E. McGaugh et al.   Nature Communications

European sea bass genome and its variation provide insights into adaptation to euryhalinity and speciation

(2014) Mbaye Tine et al.   Nature Communications

The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates

(2014) Camille Berthelot et al.   Nature Communications

Model of gene expression in extreme cold - reference transcriptome for the high-Antarctic cryopelagic notothenioid fish Pagothenia borchgrevinki

(2013) Kevin T Bilyk et al.   BMC GENOMICS

An updated view on the role of dopamine in myopia

(2013) Marita Feldkaemper et al.   EXPERIMENTAL EYE RESEARCH

Adaptive evolution of fish hatching enzyme: one amino acid substitution results in differential salt dependency of the enzyme

(2013) M. Kawaguchi et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

Genome duplication and multiple evolutionary origins of complex migratory behavior in Salmonidae

(2013) Markos A. Alexandrou et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

A systematic genome-wide analysis of zebrafish protein-coding gene function

(2013) Ross N. W. Kettleborough et al.   NATURE

The zebrafish reference genome sequence and its relationship to the human genome

(2013) Kerstin Howe et al.   NATURE

The genome of the platyfish, Xiphophorus maculatus, provides insights into evolutionary adaptation and several complex traits

(2013) Manfred Schartl et al.   NATURE GENETICS

Evolutionary changes of multiple visual pigment genes in the complete genome of Pacific bluefin tuna

(2013) Y. Nakamura et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Efficient assembly and annotation of the transcriptome of catfish by RNA-Seq analysis of a doubled haploid homozygote

(2012) Shikai Liu et al.   BMC GENOMICS

Transcriptome analysis reveals the time of the fourth round of genome duplication in common carp (Cyprinus carpio)

(2012) Jin-Tu Wang et al.   BMC GENOMICS

First draft genome sequence of the Japanese eel, Anguilla japonica

(2012) Christiaan V. Henkel et al.   GENE

Genome Evolution in the Cold: Antarctic Icefish Muscle Transcriptome Reveals Selective Duplications Increasing Mitochondrial Function

(2012) Alessandro Coppe et al.   Genome Biology and Evolution

Incorporating RNA-seq data into the zebrafish Ensembl genebuild

(2012) J. E. Collins et al.   GENOME RESEARCH

The genomic basis of adaptive evolution in threespine sticklebacks

(2012) Felicity C. Jones et al.   NATURE

RNA-Seq Identifies SNP Markers for Growth Traits in Rainbow Trout

(2012) Mohamed Salem et al.   PLoS One

Transcriptomics and Comparative Analysis of Three Antarctic Notothenioid Fishes

(2012) Seung Chul Shin et al.   PLoS One

A Y-linked anti-Mullerian hormone duplication takes over a critical role in sex determination

(2012) R. S. Hattori et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Resolution of ray-finned fish phylogeny and timing of diversification

(2012) T. J. Near et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamic evolution of venom proteins in squamate reptiles

(2012) Nicholas R. Casewell et al.   Nature Communications

Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis

(2011) A. Pauli et al.   GENOME RESEARCH

Zebrafish mRNA sequencing deciphers novelties in transcriptome dynamics during maternal to zygotic transition

(2011) Håvard Aanes et al.   GENOME RESEARCH

Opsin gene duplication and divergence in ray-finned fish

(2011) Diana J. Rennison et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The genome sequence of Atlantic cod reveals a unique immune system

(2011) Bastiaan Star et al.   NATURE

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Development of a SNP resource and a genetic linkage map for Atlantic cod (Gadus morhua)

(2010) Sophie Hubert et al.   BMC GENOMICS

Genome enablement of the notothenioidei: genome size estimates from 11 species and BAC libraries from 2 Representative Taxa

(2010) H. William Detrich et al.   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

The evolution of gene duplications: classifying and distinguishing between models

(2010) Hideki Innan et al.   NATURE REVIEWS GENETICS

Applications of antimicrobial peptides from fish and perspectives for the future

(2010) Venugopal Rajanbabu et al.   PEPTIDES

The biology and ecology of the ocean sunfish Mola mola: a review of current knowledge and future research perspectives

(2010) Edward C. Pope et al.   REVIEWS IN FISH BIOLOGY AND FISHERIES

Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags

(2010) Paul A. Hohenlohe et al.   PLoS Genetics

Pigmentation Pathway Evolution after Whole-Genome Duplication in Fish

(2009) Ingo Braasch et al.   Genome Biology and Evolution

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

SuperSAGE: A Modern Platform for Genome-Wide Quantitative Transcript Profiling

(2008) Hideo Matsumura et al.   CURRENT PHARMACEUTICAL BIOTECHNOLOGY

Molecular Basis of Spectral Tuning in the Red- and Green-Sensitive (M/LWS) Pigments in Vertebrates

(2008) S. Yokoyama et al.   GENETICS

RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays

(2008) J. C. Marioni et al.   GENOME RESEARCH

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Transcriptomic and genomic evolution under constant cold in Antarctic notothenioid fish

(2008) Z. Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Natural Selection on a Major Armor Gene in Threespine Stickleback

(2008) R. D. H. Barrett et al.   SCIENCE

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE