Sequencing, De Novo Assembly, and Annotation of the Transcriptome of the Endangered Freshwater Pearl Bivalve, Cristaria plicata, Provides Novel Insights into Functional Genes and Marker Discovery
出版年份 2016 全文链接
标题
Sequencing, De Novo Assembly, and Annotation of the Transcriptome of the Endangered Freshwater Pearl Bivalve, Cristaria plicata, Provides Novel Insights into Functional Genes and Marker Discovery
作者
关键词
Transcriptome analysis, Protein domains, Sequence motif analysis, Gene ontologies, Sequence databases, Molluscs, Sequence assembly tools, Immune response
出版物
PLoS One
Volume 11, Issue 2, Pages e0148622
出版商
Public Library of Science (PLoS)
发表日期
2016-02-13
DOI
10.1371/journal.pone.0148622
参考文献
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。- Transcriptome sequencing and annotation of the polychaete Hermodice carunculata (Annelida, Amphinomidae)
- (2015) Shaadi Mehr et al. BMC GENOMICS
- Lectin-like molecules in transcriptome of Littorina littorea hemocytes
- (2015) Alexander M. Gorbushin et al. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY
- Immune and stress responses in oysters with insights on adaptation
- (2015) Ximing Guo et al. FISH & SHELLFISH IMMUNOLOGY
- Evaluation of the population structure and genetic diversity of Plasmodium falciparum in southern China
- (2015) Guiying Wei et al. MALARIA JOURNAL
- Deep mRNA Sequencing of the Tritonia diomedea Brain Transcriptome Provides Access to Gene Homologues for Neuronal Excitability, Synaptic Transmission and Peptidergic Signalling
- (2015) Adriano Senatore et al. PLoS One
- Molecular Signatures Discriminating the Male and the Female Sexual Pathways in the Pearl Oyster Pinctada margaritifera
- (2015) Vaihiti Teaniniuraitemoana et al. PLoS One
- Sequencing and De Novo Assembly of the Gonadal Transcriptome of the Endangered Chinese Sturgeon (Acipenser sinensis)
- (2015) Huamei Yue et al. PLoS One
- De novo Transcriptome Assemblies of Rana (Lithobates) catesbeiana and Xenopus laevis Tadpole Livers for Comparative Genomics without Reference Genomes
- (2015) Inanc Birol et al. PLoS One
- Transcriptomics Analysis of Crassostrea hongkongensis for the Discovery of Reproduction-Related Genes
- (2015) Ying Tong et al. PLoS One
- SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads
- (2014) Y. Xie et al. BIOINFORMATICS
- De novoassembly, gene annotation, and simple sequence repeat marker development using Illumina paired-end transcriptome sequences in the pearl oysterPinctada maxima
- (2014) Yuewen Deng et al. BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY
- De novo transcriptome analysis of Perna viridis highlights tissue-specific patterns for environmental studies
- (2014) Priscilla TY Leung et al. BMC GENOMICS
- Gonad transcriptome analysis of pearl oyster Pinctada margaritifera: identification of potential sex differentiation and sex determining genes
- (2014) Vaihiti Teaniniuraitemoana et al. BMC GENOMICS
- Regulation of male sex determination: genital ridge formation and Sry activation in mice
- (2014) Satomi S. Tanaka et al. CELLULAR AND MOLECULAR LIFE SCIENCES
- Toll signal transduction pathway in bivalves: Complete cds of intermediate elements and related gene transcription levels in hemocytes of immune stimulated Mytilus galloprovincialis
- (2014) Mylène Toubiana et al. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY
- Molecular cloning and characterization of cathepsin L from freshwater mussel, Cristaria plicata
- (2014) Xiaojuan Hu et al. FISH & SHELLFISH IMMUNOLOGY
- Deep transcriptome sequencing of Pecten maximus hemocytes: A genomic resource for bivalve immunology
- (2014) Marianna Pauletto et al. FISH & SHELLFISH IMMUNOLOGY
- Expression Analysis of Immune Related Genes Identified from the Coelomocytes of Sea Cucumber (Apostichopus japonicus) in Response to LPS Challenge
- (2014) Ying Dong et al. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
- De Novo Transcriptome Sequencing of the Snail Echinolittorina malaccana: Identification of Genes Responsive to Thermal Stress and Development of Genetic Markers for Population Studies
- (2014) Wei Wang et al. MARINE BIOTECHNOLOGY
- The Anadara trapezia transcriptome: A resource for molluscan physiological genomics
- (2014) Peter J. Prentis et al. Marine Genomics
- Deep sequencing of the mantle transcriptome of the great scallop Pecten maximus
- (2014) Sébastien Artigaud et al. Marine Genomics
- Transcriptomic Analysis of Endangered Chinese Salamander: Identification of Immune, Sex and Reproduction-Related Genes and Genetic Markers
- (2014) Rongbo Che et al. PLoS One
- Gene Discovery through Transcriptome Sequencing for the Invasive Mussel Limnoperna fortunei
- (2014) Marcela Uliano-Silva et al. PLoS One
- De Novo Transcriptome Sequencing of the Octopus vulgaris Hemocytes Using Illumina RNA-Seq Technology: Response to the Infection by the Gastrointestinal Parasite Aggregata octopiana
- (2014) Sheila Castellanos-Martínez et al. PLoS One
- Identification of 246 microsatellites in the Asiatic clam (Corbicula fluminea)
- (2014) Luis Peñarrubia et al. Conservation Genetics Resources
- Assessing mechanisms of toxicant response in the amphipod Melita plumulosa through transcriptomic profiling
- (2013) Sharon E. Hook et al. AQUATIC TOXICOLOGY
- Transcriptome sequencing and de novo annotation of the critically endangered Adriatic sturgeon
- (2013) Michele Vidotto et al. BMC GENOMICS
- Gene identification and recombinant protein of a lysozyme from freshwater mussel Cristaria plicata
- (2013) Dan Wu et al. FISH & SHELLFISH IMMUNOLOGY
- Genomic organization, sequence characterization and expression analysis of Tenebrio molitor apolipophorin-III in response to an intracellular pathogen, Listeria monocytogenes
- (2013) Ju Young Noh et al. GENE
- Cloning, Characterization and Effect of TmPGRP-LE Gene Silencing on Survival of Tenebrio Molitor against Listeria monocytogenes Infection
- (2013) Hamisi Tindwa et al. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
- Characterization of the Zhikong Scallop (Chlamys farreri) Mantle Transcriptome and Identification of Biomineralization-Related Genes
- (2013) Mingjun Shi et al. MARINE BIOTECHNOLOGY
- Transcriptome Analysis Reveals a Rich Gene Set Related to Innate Immunity in the Eastern Oyster (Crassostrea virginica)
- (2013) Linlin Zhang et al. MARINE BIOTECHNOLOGY
- De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis
- (2013) Brian J Haas et al. Nature Protocols
- Transcriptome Analysis of Pacific White Shrimp (Litopenaeus vannamei) Hepatopancreas in Response to Taura Syndrome Virus (TSV) Experimental Infection
- (2013) Digang Zeng et al. PLoS One
- De Novo Characterization of Japanese Scallop Mizuhopecten yessoensis Transcriptome and Analysis of Its Gene Expression following Cadmium Exposure
- (2013) Xiao-lin Meng et al. PLoS One
- De Novo Assembly and Characterization of Two Transcriptomes Reveal Multiple Light-Mediated Functions in the Scallop Eye (Bivalvia: Pectinidae)
- (2013) Autum N. Pairett et al. PLoS One
- Identification of Male Gametogenesis Expressed Genes from the Scallop Nodipecten subnodosus by Suppressive Subtraction Hybridization and Pyrosequencing
- (2013) Raúl Llera-Herrera et al. PLoS One
- Transcriptome Profile of the Green Odorous Frog (Odorrana margaretae)
- (2013) Liang Qiao et al. PLoS One
- Sequencing and De Novo Assembly of the Asian Clam (Corbicula fluminea) Transcriptome Using the Illumina GAIIx Method
- (2013) Huihui Chen et al. PLoS One
- Characteristic and Functional Analysis of Toll-like Receptors (TLRs) in the lophotrocozoan, Crassostrea gigas, Reveals Ancient Origin of TLR-Mediated Innate Immunity
- (2013) Yang Zhang et al. PLoS One
- Reproduction-Related Genes in the Pearl Oyster Genome
- (2013) Toshie Matsumoto et al. ZOOLOGICAL SCIENCE
- Diversity in recognition of glycans by F-type lectins and galectins: molecular, structural, and biophysical aspects
- (2012) Gerardo R. Vasta et al. Annals of the New York Academy of Sciences
- Discovery and characterization of microsatellites for the solitary bee Colletes inaequalis using Sanger and 454 pyrosequencing
- (2012) Margarita M. López-Uribe et al. APIDOLOGIE
- Molecular characterization and immune analysis of a defensin from freshwater pearl mussel, Hyriopsis schlegelii
- (2012) Kou Peng et al. AQUACULTURE
- Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels
- (2012) Marcel H. Schulz et al. BIOINFORMATICS
- Molecular cloning, characterization and expression of heat shock protein 70 gene from the oyster Crassostrea hongkongensis responding to thermal stress and exposure of Cu2+ and malachite green
- (2012) Zhanhui Zhang et al. GENE
- Exploring the Transcriptome of Atlantic Salmon (Salmo salar) Skin, a Major Defense Organ
- (2012) Giulia Micallef et al. MARINE BIOTECHNOLOGY
- Mitochondrial genome of the cockscomb pearl musselCristaria plicata(Bivalvia, Unionoida, Unionidae)
- (2012) Jin Hee Lee et al. Mitochondrial DNA
- The oyster genome reveals stress adaptation and complexity of shell formation
- (2012) Guofan Zhang et al. NATURE
- Defining the limits of physiological plasticity: how gene expression can assess and predict the consequences of ocean change
- (2012) T. G. Evans et al. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
- Massively Parallel RNA Sequencing Identifies a Complex Immune Gene Repertoire in the lophotrochozoan Mytilus edulis
- (2012) Eva E. R. Philipp et al. PLoS One
- Transcriptome Analysis of the Oriental River Prawn, Macrobrachium nipponense Using 454 Pyrosequencing for Discovery of Genes and Markers
- (2012) Keyi Ma et al. PLoS One
- Pyrosequencing of Haliotis diversicolor Transcriptomes: Insights into Early Developmental Molluscan Gene Expression
- (2012) Zi-Xia Huang et al. PLoS One
- Dmrt genes in the development and evolution of sexual dimorphism
- (2012) Artyom Kopp TRENDS IN GENETICS
- Understanding the Role of Host Hemocytes in a Squid/Vibrio Symbiosis Using Transcriptomics and Proteomics
- (2012) Andrew J. Collins et al. Frontiers in Immunology
- De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweetpotato (Ipomoea batatas)
- (2011) Zhangying Wang et al. BMC GENOMICS
- Short read Illumina data for the de novo assembly of a non-model snail species transcriptome (Radix balthica, Basommatophora, Pulmonata), and a comparison of assembler performance
- (2011) Barbara Feldmeyer et al. BMC GENOMICS
- Transcriptome sequencing and microarray development for the Manila clam, Ruditapes philippinarum: genomic tools for environmental monitoring
- (2011) Massimo Milan et al. BMC GENOMICS
- Insights into the innate immunity of the Mediterranean mussel Mytilus galloprovincialis
- (2011) Paola Venier et al. BMC GENOMICS
- A comprehensive transcriptome and immune-gene repertoire of the lepidopteran model host Galleria mellonella
- (2011) Heiko Vogel et al. BMC GENOMICS
- Six defensins from the triangle-shell pearl mussel Hyriopsis cumingii
- (2011) Qian Ren et al. FISH & SHELLFISH IMMUNOLOGY
- A novel C-type lectin from bay scallop Argopecten irradians (AiCTL-7) agglutinating fungi with mannose specificity
- (2011) Pengfei Kong et al. FISH & SHELLFISH IMMUNOLOGY
- A catalase from the freshwater mussel Cristaria plicata with cloning, identification and protein characterization
- (2011) Yang Xilan et al. FISH & SHELLFISH IMMUNOLOGY
- cDNA cloning and mRNA expression of a tandem-repeat galectin (PoGal2) from the pearl oyster, Pinctada fucata
- (2011) D.C. Zhang et al. GENETICS AND MOLECULAR RESEARCH
- Determination of Gender in the Pearl OysterPinctada margaritifera
- (2011) Jorge Chávez-Villalba et al. JOURNAL OF SHELLFISH RESEARCH
- Molecular Cloning and Expression Characterization ofDmrt2in Akoya Pearl Oysters,Pinctada martensii
- (2011) Fei-Fei Yu et al. JOURNAL OF SHELLFISH RESEARCH
- Resolving the evolutionary relationships of molluscs with phylogenomic tools
- (2011) Stephen A. Smith et al. NATURE
- Full-length transcriptome assembly from RNA-Seq data without a reference genome
- (2011) Manfred G Grabherr et al. NATURE BIOTECHNOLOGY
- New Insights into the Apoptotic Process in Mollusks: Characterization of Caspase Genes in Mytilus galloprovincialis
- (2011) Alejandro Romero et al. PLoS One
- Transcriptome Sequencing and De Novo Analysis for Yesso Scallop (Patinopecten yessoensis) Using 454 GS FLX
- (2011) Rui Hou et al. PLoS One
- Molecular Cloning and Copy Number Variation of a Ferritin Subunit (Fth1) and Its Association with Growth in Freshwater Pearl Mussel Hyriopsis cumingii
- (2011) Zhiyi Bai et al. PLoS One
- Transcriptomics of a Giant Freshwater Prawn (Macrobrachium rosenbergii): De Novo Assembly, Annotation and Marker Discovery
- (2011) Hyungtaek Jung et al. PLoS One
- Development and characterization of EST-SSR markers in the invasive weed Mikania micrantha (Asteraceae)
- (2010) Y. Yan et al. AMERICAN JOURNAL OF BOTANY
- Manipulation of FASTQ data with Galaxy
- (2010) D. Blankenberg et al. BIOINFORMATICS
- Insights into shell deposition in the Antarctic bivalve Laternula elliptica: gene discovery in the mantle transcriptome using 454 pyrosequencing
- (2010) Melody S Clark et al. BMC GENOMICS
- Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads
- (2010) Jeffrey Martin et al. BMC GENOMICS
- Sry: the master switch in mammalian sex determination
- (2010) K. Kashimada et al. DEVELOPMENT
- Molecular characterization and expression analysis of cathepsin L1 cysteine protease from pearl oyster Pinctada fucata
- (2010) Jianjun Ma et al. FISH & SHELLFISH IMMUNOLOGY
- Insight into Invertebrate Defensin Mechanism of Action
- (2010) Paulina Schmitt et al. JOURNAL OF BIOLOGICAL CHEMISTRY
- Phagocytosis of the protozoan parasite, Marteilia sydneyi, by Sydney rock oyster (Saccostrea glomerata) hemocytes
- (2010) Rhiannon P. Kuchel et al. JOURNAL OF INVERTEBRATE PATHOLOGY
- De novo assembly and analysis of RNA-seq data
- (2010) Gordon Robertson et al. NATURE METHODS
- MytiBase: a knowledgebase of mussel (M. galloprovincialis) transcribed sequences
- (2009) Paola Venier et al. BMC GENOMICS
- Molecular cloning and gene expression of Cg-Foxl2 during the development and the adult gametogenetic cycle in the oyster Crassostrea gigas
- (2009) Amine Naimi et al. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY B-BIOCHEMISTRY & MOLECULAR BIOLOGY
- Noble tandem-repeat galectin of Manila clam Ruditapes philippinarum is induced upon infection with the protozoan parasite Perkinsus olseni
- (2008) Jin Young Kim et al. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY
- Molecular cloning and gene expression of Foxl2 in the frog Rana rugosa
- (2008) Yuki Oshima et al. GENERAL AND COMPARATIVE ENDOCRINOLOGY
- Analysis of Genes Isolated from Plated Hemocytes of the Pacific Oyster, Crassostreas gigas
- (2008) Steven Roberts et al. MARINE BIOTECHNOLOGY
- Amplification of rainbow trout microsatellites inBrachymystax lenok
- (2008) Z. Y. JIA et al. Molecular Ecology Resources
- Use and misuse of the gene ontology annotations
- (2008) Seung Yon Rhee et al. NATURE REVIEWS GENETICS
- Characterization of reproduction-specific genes in a marine bivalve mollusc: Influence of maturation stage and sex on mRNA expression
- (2007) Isabelle Boutet et al. GENE
Add your recorded webinar
Do you already have a recorded webinar? Grow your audience and get more views by easily listing your recording on Peeref.
Upload NowBecome a Peeref-certified reviewer
The Peeref Institute provides free reviewer training that teaches the core competencies of the academic peer review process.
Get Started