| 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 Publication | DNA RESEARCH
 |
| ISSN | 1340-2838 |
| Volume | 19Issue:2Pages:131-142 |
| Abstract | 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.; 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. |
| Subtype | Article |
| Keyword | Silver 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 |
| DOI | 10.1093/dnares/dsr046 |
| WOS Headings | Science & Technology ; Life Sciences & Biomedicine |
| Funding Organization | 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] ; 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 By | SCI |
| Language | 英语 |
| WOS Research Area | Genetics & Heredity |
| WOS Subject | Genetics & Heredity |
| WOS ID | WOS:000303290100003 |
| WOS Keyword | TOXIC MICROCYSTIS BLOOMS ; CAJANUS-CAJAN L. ; SSR-MARKERS ; LAKE TAIHU ; IN-SITU ; GENOME ; ANNOTATION ; GENERATION ; REVEALS ; FISH |
| Funding Organization | 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] ; 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 | |
| Document Type | 期刊论文 |
| Identifier | http://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 Author | He, SP (reprint author), Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, Wuhan 430072, Peoples R China. |
| Affiliation | 1.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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| Transcriptome Analys（356KB） | 开放获取 | -- | View Application Full Text | |||
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