IHB OpenIR  > 水生生物多样性与资源保护研究中心  > 期刊论文
Transcriptome Analysis of Silver Carp (Hypophthalmichthys molitrix) by Paired-End RNA Sequencing
Fu, Beide1,2; He, Shunping1; He, SP (reprint author), Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, Wuhan 430072, Peoples R China.
2012-04-01
Source PublicationDNA RESEARCH
ISSN1340-2838
Volume19Issue:2Pages:131-142
AbstractThe silver carp (Hypophthalmichthys molitrix) is among the most intensively pond-cultured fish species and is used in the wild to counteract water bloom in China. However, little genomic information is available for this species, especially regarding its ability to grow rapidly in water, even water contaminated with high concentrations of poisonous microcystin. In this study, we performed de novo transcriptome assembly and analysis of the 17.10 million short-read sequences produced by the Illumina paired-end sequencing technology. Using an improved multiple k-mer contig assembly method coupled with further scaffolding, 85 759 sequences were obtained. There were 23 044 sequences annotated with 3423 gene ontology terms for 104 196 term occurrences and the three corresponding organizing principles. A total of 38 200 assembled sequences were involved in 218 predicted Kyoto Encyclopedia of Genes and Genomes metabolic pathways. We also recovered 41 of 44 genes involved in the biosynthesis of glutathione. Of these, five genes were identified as experienced positive selection between silver carp and zebrafish, as determined by the likelihood ratio test. This report is the first annotated review of the silver carp transcriptome. These data will be of interest to researchers investigating the evolution and biological processes of the silver carp. This work also provides an archive for future studies of recent speciation and evolution of Cyprinidae fishes and can be used in comparative studies of other fishes.; The silver carp (Hypophthalmichthys molitrix) is among the most intensively pond-cultured fish species and is used in the wild to counteract water bloom in China. However, little genomic information is available for this species, especially regarding its ability to grow rapidly in water, even water contaminated with high concentrations of poisonous microcystin. In this study, we performed de novo transcriptome assembly and analysis of the 17.10 million short-read sequences produced by the Illumina paired-end sequencing technology. Using an improved multiple k-mer contig assembly method coupled with further scaffolding, 85 759 sequences were obtained. There were 23 044 sequences annotated with 3423 gene ontology terms for 104 196 term occurrences and the three corresponding organizing principles. A total of 38 200 assembled sequences were involved in 218 predicted Kyoto Encyclopedia of Genes and Genomes metabolic pathways. We also recovered 41 of 44 genes involved in the biosynthesis of glutathione. Of these, five genes were identified as experienced positive selection between silver carp and zebrafish, as determined by the likelihood ratio test. This report is the first annotated review of the silver carp transcriptome. These data will be of interest to researchers investigating the evolution and biological processes of the silver carp. This work also provides an archive for future studies of recent speciation and evolution of Cyprinidae fishes and can be used in comparative studies of other fishes.
SubtypeArticle
KeywordSilver Carp Transcriptome Paired-end Rna Sequencing
Department[Fu, Beide; He, Shunping] Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, Wuhan 430072, Peoples R China; [Fu, Beide] Chinese Acad Sci, Grad Univ, Beijing 100039, Peoples R China
DOI10.1093/dnares/dsr046
WOS HeadingsScience & Technology ; Life Sciences & Biomedicine
Funding OrganizationNational Basic Research Program of China (973 Program)[2010CB126302]; National Natural Science Foundation of China[31090254, U1036603]; Chinese Academy of Sciences[KSCX2-EW-Q-12] ; National Basic Research Program of China (973 Program)[2010CB126302]; National Natural Science Foundation of China[31090254, U1036603]; Chinese Academy of Sciences[KSCX2-EW-Q-12] ; National Basic Research Program of China (973 Program)[2010CB126302]; National Natural Science Foundation of China[31090254, U1036603]; Chinese Academy of Sciences[KSCX2-EW-Q-12] ; National Basic Research Program of China (973 Program)[2010CB126302]; National Natural Science Foundation of China[31090254, U1036603]; Chinese Academy of Sciences[KSCX2-EW-Q-12]
Indexed BySCI
Language英语
WOS Research AreaGenetics & Heredity
WOS SubjectGenetics & Heredity
WOS IDWOS:000303290100003
WOS KeywordTOXIC MICROCYSTIS BLOOMS ; CAJANUS-CAJAN L. ; SSR-MARKERS ; LAKE TAIHU ; IN-SITU ; GENOME ; ANNOTATION ; GENERATION ; REVEALS ; FISH
Funding OrganizationNational Basic Research Program of China (973 Program)[2010CB126302]; National Natural Science Foundation of China[31090254, U1036603]; Chinese Academy of Sciences[KSCX2-EW-Q-12] ; National Basic Research Program of China (973 Program)[2010CB126302]; National Natural Science Foundation of China[31090254, U1036603]; Chinese Academy of Sciences[KSCX2-EW-Q-12] ; National Basic Research Program of China (973 Program)[2010CB126302]; National Natural Science Foundation of China[31090254, U1036603]; Chinese Academy of Sciences[KSCX2-EW-Q-12] ; National Basic Research Program of China (973 Program)[2010CB126302]; National Natural Science Foundation of China[31090254, U1036603]; Chinese Academy of Sciences[KSCX2-EW-Q-12]
Citation statistics
Cited Times:46[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.ihb.ac.cn/handle/342005/16809
Collection水生生物多样性与资源保护研究中心_期刊论文
Corresponding AuthorHe, SP (reprint author), Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, Wuhan 430072, Peoples R China.
Affiliation1.Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, Wuhan 430072, Peoples R China
2.Chinese Acad Sci, Grad Univ, Beijing 100039, Peoples R China
Recommended Citation
GB/T 7714
Fu, Beide,He, Shunping,He, SP . Transcriptome Analysis of Silver Carp (Hypophthalmichthys molitrix) by Paired-End RNA Sequencing[J]. DNA RESEARCH,2012,19(2):131-142.
APA Fu, Beide,He, Shunping,&He, SP .(2012).Transcriptome Analysis of Silver Carp (Hypophthalmichthys molitrix) by Paired-End RNA Sequencing.DNA RESEARCH,19(2),131-142.
MLA Fu, Beide,et al."Transcriptome Analysis of Silver Carp (Hypophthalmichthys molitrix) by Paired-End RNA Sequencing".DNA RESEARCH 19.2(2012):131-142.
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