Aquaculture omics: An update on the current status of research and data analysis

RNA-Seq Transcriptome Analysis of the Liver and Brain of the Black Carp (Mylopharyngodon piceus) During Fasting

(2021) Ya-Fan Dai et al.   MARINE BIOTECHNOLOGY

De novo Assembly and Genome-Wide SNP Discovery in Rohu Carp, Labeo rohita

(2020) Paramananda Das et al.   Frontiers in Genetics

The genome of walking catfish Clarias magur (Hamilton, 1822) unveils the genetic basis that may have facilitated the development of environmental and terrestrial adaptation systems in air-breathing catfishes

(2020) Basdeo Kushwaha et al.   DNA RESEARCH

Transcriptome-wide changes associated with the reproductive behaviour of male guppies exposed to 17α-ethinyl estradiol

(2020) Minna Saaristo et al.   ENVIRONMENTAL POLLUTION

Transcriptome Profile Analysis on Ovarian Tissues of Autotetraploid Fish and Diploid Red Crucian Carp

(2019) Yude Wang et al.   Frontiers in Genetics

Transcriptome Analysis of Male and Female Mature Gonads of Silver Sillago (Sillago sihama)

(2019) Changxu Tian et al.   Genes

Constructing a High-Density Genetic Linkage Map for Large Yellow Croaker (Larimichthys crocea) and Mapping Resistance Trait Against Ciliate Parasite Cryptocaryon irritans

(2019) Shengnan Kong et al.   MARINE BIOTECHNOLOGY

Complete genome sequence and pathogenic analysis of a new betanodavirus isolated from shellfish

(2019) Young Chul Kim et al.   JOURNAL OF FISH DISEASES

Revealing liver specific microRNAs linked with carbohydrate metabolism of farmed carp, Labeo rohita (Hamilton, 1822)

(2019) Kiran D. Rasal et al.   GENOMICS

Liver-Specific microRNA Identification in Farmed Carp, Labeo bata (Hamilton, 1822), Fed with Starch Diet Using High-Throughput Sequencing

(2019) Kiran D. Rasal et al.   MARINE BIOTECHNOLOGY

Genomic and Metagenomic Insights Into the Microbial Community in the Regenerating Intestine of the Sea Cucumber Apostichopus japonicus

(2019) Hongxia Zhang et al.   Frontiers in Microbiology

Inventory of European Sea Bass (Dicentrarchus labrax) sncRNAs Vital During Early Teleost Development

(2019) Elena Sarropoulou et al.   Frontiers in Genetics

De novo assembly of the goldfish (Carassius auratus) genome and the evolution of genes after whole-genome duplication

(2019) Zelin Chen et al.   Science Advances

Species-Specific Marker Discovery in Tilapia

(2019) Mochamad Syaifudin et al.   Scientific Reports

Metagenomics Reveals Seasonal Functional Adaptation of the Gut Microbiome to Host Feeding and Fasting in the Chinese Alligator

(2019) Ke-Yi Tang et al.   Frontiers in Microbiology

Regulatory Pathways Controlling Female Insect Reproduction

(2018) Sourav Roy et al.   Annual Review of Entomology

RNA-Seq analysis of transcriptome responses in Atlantic cod ( Gadus morhua ) precision-cut liver slices exposed to benzo[ a ]pyrene and 17α-ethynylestradiol

(2018) Fekadu Yadetie et al.   AQUATIC TOXICOLOGY

A comparative genomics study of carbohydrate/glucose metabolic genes: from fish to mammals

(2018) Yuru Zhang 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

Length-weight relationships for three fishes in the Mali Hka River and Nmai Hka River, Myanmar

(2018) Hai-Tao Zheng et al.   JOURNAL OF APPLIED ICHTHYOLOGY

Metagenomic sequencing of environmental DNA reveals marine faunal assemblages from the West Antarctic Peninsula

(2018) Dominique A. Cowart et al.   Marine Genomics

Dietary soybean meal affects intestinal homoeostasis by altering the microbiota, morphology and inflammatory cytokine gene expression in northern snakehead

(2018) Shuyan Miao et al.   Scientific Reports

Application of omics technologies for a deeper insight into quali-quantitative production traits in broiler chickens: A review

(2018) Marco Zampiga et al.   Journal of Animal Science and Biotechnology

MicroRNA Alternations in the Testes Related to the Sterility of Triploid Fish

(2018) Min Tao et al.   MARINE BIOTECHNOLOGY

Detailed insights into pan-European population structure and inbreeding in wild and hatchery Pacific oysters (Crassostrea gigas ) revealed by genome-wide SNP data

(2018) David L. J. Vendrami et al.   Evolutionary Applications

Gonadal transcriptome analysis of the common carp, Cyprinus carpio: Identification of differentially expressed genes and SSRs

(2018) Arumugam Anitha et al.   GENERAL AND COMPARATIVE ENDOCRINOLOGY

Comparative study of gut microbiota in wild and captive Malaysian Mahseer (Tor tambroides )

(2018) Chun K. Tan et al.   MicrobiologyOpen

Transcriptomic analysis of immunity in rainbow trout (Oncorhynchus mykiss) gills infected by Ichthyophthirius multifiliis

(2018) Khairul Syahputra et al.   FISH & SHELLFISH IMMUNOLOGY

Applications of next-generation sequencing in fisheries research: A review

(2017) Girish Kumar et al.   FISHERIES RESEARCH

Temporal variation in brain transcriptome is associated with the expression of female mimicry as a sequential male alternative reproductive tactic in fish

(2017) Sara D. Cardoso et al.   MOLECULAR ECOLOGY

Assessment of Common and Emerging Bioinformatics Pipelines for Targeted Metagenomics

(2017) Léa Siegwald et al.   PLoS One

The skin microbiome of the common thresher shark (Alopias vulpinus ) has low taxonomic and gene function β-diversity

(2017) Michael P. Doane et al.   Environmental Microbiology Reports

Discovery and characterization of single nucleotide polymorphisms in two anadromous alosine fishes of conservation concern

(2017) Diana S. Baetscher et al.   Ecology and Evolution

Enhancing the Resolution of Rumen Microbial Classification from Metatranscriptomic Data Using Kraken and Mothur

(2017) Andre L. A. Neves et al.   Frontiers in Microbiology

Parasitism perturbs the mucosal microbiome of Atlantic Salmon

(2017) M. S. Llewellyn et al.   Scientific Reports

Supplementation of formulated diets for tilapia (Oreochromis niloticus) with selected exogenous enzymes: Overall performance and effects on intestinal histology and microbiota

(2016) A.A. Adeoye et al.   ANIMAL FEED SCIENCE AND TECHNOLOGY

Transcriptome profiling in fast versus slow-growing rainbow trout across seasonal gradients

(2016) Roy G. Danzmann et al.   BMC GENOMICS

Characterization of an extensive rainbow trout miRNA transcriptome by next generation sequencing

(2016) Amelie Juanchich et al.   BMC GENOMICS

Whole genome sequencing of turbot (Scophthalmus maximus; Pleuronectiformes): a fish adapted to demersal life

(2016) Antonio Figueras et al.   DNA RESEARCH

Atlantic Salmon (Salmo salar L.) Gastrointestinal Microbial Community Dynamics in Relation to Digesta Properties and Diet

(2016) Kamarul Zaman Zarkasi et al.   MICROBIAL ECOLOGY

IMG/M: integrated genome and metagenome comparative data analysis system

(2016) I-Min A. Chen et al.   NUCLEIC ACIDS RESEARCH

Fish intake during pregnancy or infancy and allergic outcomes in children: A systematic review and meta-analysis

(2016) Guo-Qiang Zhang et al.   PEDIATRIC ALLERGY AND IMMUNOLOGY

Next generation sequencing technology and genomewide data analysis: Perspectives for retinal research

(2016) Vijender Chaitankar et al.   PROGRESS IN RETINAL AND EYE RESEARCH

Hypoxia causes transgenerational impairments in reproduction of fish

(2016) Simon Yuan Wang et al.   Nature Communications

SNP discovery from liver transcriptome in the fish Piaractus mesopotamicus

(2016) Vito Antonio Mastrochirico-Filho et al.   Conservation Genetics Resources

Identification of Deleterious Mutations inMyostatinGene of Rohu Carp (Labeo rohita) Using Modeling and Molecular Dynamic Simulation Approaches

(2016) Kiran Dashrath Rasal et al.   Biomed Research International

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

(2016) Ying Sun et al.   GigaScience

Liver Transcriptome Analysis of the Large Yellow Croaker (Larimichthys crocea) during Fasting by Using RNA-Seq

(2016) Baoying Qian et al.   PLoS One

Transcriptome Analysis of the Innate Immunity-Related Complement System in Spleen Tissue of Ctenopharyngodon idella Infected with Aeromonas hydrophila

(2016) Yunfei Dang et al.   PLoS One

Co-cultivation and transcriptome sequencing of two co-existing fish pathogens Moritella viscosa and Aliivibrio wodanis

(2015) Erik Hjerde et al.   BMC GENOMICS

Temperature during early development has long-term effects on microRNA expression in Atlantic cod

(2015) Teshome Tilahun Bizuayehu et al.   BMC GENOMICS

Identification of microRNA biomarkers in type 2 diabetes: a meta-analysis of controlled profiling studies

(2015) Hongmei Zhu et al.   DIABETOLOGIA

Assessment of immunotoxicity of dibutyl phthalate using live zebrafish embryos

(2015) Hai Xu et al.   FISH & SHELLFISH IMMUNOLOGY

A comparative study on microbiota from the intestine of Prussian carp (Carassius gibelio) and their aquatic environmental compartments, using different molecular methods

(2015) E.N. Kashinskaya et al.   JOURNAL OF APPLIED MICROBIOLOGY

RNA Sequencing to Study Gene Expression and SNP Variations Associated with Growth in Zebrafish Fed a Plant Protein-Based Diet

(2015) Pilar E. Ulloa et al.   MARINE BIOTECHNOLOGY

Jin et al. reply

(2015) F.-F. Jin et al.   NATURE

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

(2015) Yaping Wang et al.   NATURE GENETICS

Influence of Development and Dietary Phospholipid Content and Composition on Intestinal Transcriptome of Atlantic Salmon (Salmo salar)

(2015) Christian De Santis et al.   PLoS One

The outer mucus layer hosts a distinct intestinal microbial niche

(2015) Hai Li et al.   Nature Communications

Construction, De-Novo Assembly and Analysis of Transcriptome for Identification of Reproduction-Related Genes and Pathways from Rohu, Labeo rohita (Hamilton)

(2015) Dinesh Kumar Sahu et al.   PLoS One

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

(2014) Wenji Wang et al.   BMC GENOMICS

Thermal plasticity of the miRNA transcriptome during Senegalese sole development

(2014) Catarina Campos et al.   BMC GENOMICS

Mutations of 60 known causative genes in 157 families with retinitis pigmentosa based on exome sequencing

(2014) Yan Xu et al.   HUMAN GENETICS

Characterization of the gut microbiota of three commercially valuable warmwater fish species

(2014) A.M. Larsen et al.   JOURNAL OF APPLIED MICROBIOLOGY

Transcriptome Analysis of Psoriasis in a Large Case–Control Sample: RNA-Seq Provides Insights into Disease Mechanisms

(2014) Bingshan Li et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

Elephant shark genome provides unique insights into gnathostome evolution

(2014) Byrappa Venkatesh et al.   NATURE

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

RNA-Seq Technology and Its Application in Fish Transcriptomics

(2014) Xi Qian et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Clear as mud: A meta-analysis on the effects of sedimentation on freshwater fish and the effectiveness of sediment-control measures

(2014) Jacqueline M. Chapman et al.   WATER RESEARCH

Regulation of microRNA expression in the neuronal stem cell niches during aging of the short-lived annual fish Nothobranchius furzeri

(2014) Eva Terzibasi Tozzini et al.   Frontiers in Cellular Neuroscience

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

Systemic Approach to Identify Serum microRNAs as Potential Biomarkers for Acute Myocardial Infarction

(2014) An Hsu et al.   Biomed Research International

Dietary differences are reflected on the gut prokaryotic community structure of wild and commercially reared sea bream (Sparus aurata)

(2014) Konstantinos A. Kormas et al.   MicrobiologyOpen

Plasticity of gene expression according to salinity in the testis of broodstock and F1 black-chinned tilapia,Sarotherodon melanotheron heudelotii

(2014) Jean-Christophe Avarre et al.   PeerJ

Aquacultured Rainbow Trout (Oncorhynchus mykiss) Possess a Large Core Intestinal Microbiota That Is Resistant to Variation in Diet and Rearing Density

(2013) S. Wong et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Characterization of differential transcript abundance through time during Nematostella vectensis development

(2013) Rebecca Helm et al.   BMC GENOMICS

Factors influencing the grass carp gut microbiome and its effect on metabolism

(2013) Jiajia Ni et al.   FEMS MICROBIOLOGY ECOLOGY

Fish gut microbiota analysis differentiates physiology and behavior of invasive Asian carp and indigenous American fish

(2013) Lin Ye et al.   ISME Journal

The African coelacanth genome provides insights into tetrapod evolution

(2013) Chris T. Amemiya 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

Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution

(2013) Jeramiah J Smith et al.   NATURE GENETICS

EBI metagenomics—a new resource for the analysis and archiving of metagenomic data

(2013) Sarah Hunter et al.   NUCLEIC ACIDS RESEARCH

Deep RNA Sequencing of the Skeletal Muscle Transcriptome in Swimming Fish

(2013) Arjan P. Palstra et al.   PLoS One

Gut Microbiota Contributes to the Growth of Fast-Growing Transgenic Common Carp (Cyprinus carpio L.)

(2013) Xuemei Li et al.   PLoS One

SNP Discovery in European Anchovy (Engraulis encrasicolus, L) by High-Throughput Transcriptome and Genome Sequencing

(2013) Iratxe Montes et al.   PLoS One

De novo Assembly of the Indo-Pacific Humpback Dolphin Leucocyte Transcriptome to Identify Putative Genes Involved in the Aquatic Adaptation and Immune Response

(2013) Duan Gui et al.   PLoS One

Hepatic transcriptome profiling indicates differential mRNA expression of apoptosis and immune related genes in eelpout (Zoarces viviparus) caught at Göteborg harbor, Sweden

(2012) Noomi Asker et al.   AQUATIC TOXICOLOGY

Microbiota Regulate Intestinal Absorption and Metabolism of Fatty Acids in the Zebrafish

(2012) Ivana Semova et al.   Cell Host & Microbe

Incorporating RNA-seq data into the zebrafish Ensembl genebuild

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

Differential expression patterns of growth-related microRNAs in the skeletal muscle of Nile tilapia (Oreochromis niloticus)1

(2012) C. W. Huang et al.   JOURNAL OF ANIMAL SCIENCE

Expressed Sequences and Polymorphisms in Rohu Carp (Labeo rohita, Hamilton) Revealed by mRNA-seq

(2012) Nicholas Robinson et al.   MARINE BIOTECHNOLOGY

The genomic basis of adaptive evolution in threespine sticklebacks

(2012) Felicity C. Jones et al.   NATURE

Targeted SNP discovery in Atlantic salmon (Salmo salar) genes using a 3'UTR-primed SNP detection approach

(2011) Rune Andreassen et al.   BMC GENOMICS

Generation of a reference transcriptome for evaluating rainbow trout responses to various stressors

(2011) Cecilia C Sánchez et al.   BMC GENOMICS

Effects of the total replacement of fish-based diet with plant-based diet on the hepatic transcriptome of two European sea bass (Dicentrarchus labrax) half-sibfamilies showing different growth rates with the plant-based diet

(2011) Florian Geay et al.   BMC GENOMICS

Conserved Function of lincRNAs in Vertebrate Embryonic Development despite Rapid Sequence Evolution

(2011) Igor Ulitsky et al.   CELL

Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis

(2011) A. Pauli et al.   GENOME RESEARCH

The genome sequence of Atlantic cod reveals a unique immune system

(2011) Bastiaan Star et al.   NATURE

Gene Discovery and Tissue-Specific Transcriptome Analysis in Chickpea with Massively Parallel Pyrosequencing and Web Resource Development

(2011) R. Garg et al.   PLANT PHYSIOLOGY

Metagenomic Analyses: Past and Future Trends

(2010) Carola Simon et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Mining transcriptome sequences towards identifying adaptive single nucleotide polymorphisms in lake whitefish species pairs (Coregonusspp. Salmonidae)

(2010) SÉBASTIEN RENAUT et al.   MOLECULAR ECOLOGY

Single nucleotide polymorphism discovery in rainbow trout by deep sequencing of a reduced representation library

(2009) Cecilia Sánchez et al.   BMC GENOMICS

Transcriptome Profiling and Functional Analyses of the Zebrafish Embryonic Innate Immune Response to Salmonella Infection

(2009) O. W. Stockhammer et al.   JOURNAL OF IMMUNOLOGY

A MicroRNA Repertoire for Functional Genome Research in Rainbow Trout (Oncorhynchus mykiss)

(2009) Mohamed Salem et al.   MARINE BIOTECHNOLOGY

Identification and characterisation of novel SNP markers in Atlantic cod: Evidence for directional selection

(2008) Thomas Moen et al.   BMC GENETICS