Transcriptome Analysis of Silver Carp (Hypophthalmichthys molitrix) by Paired-End RNA Sequencing
文献类型：期刊论文
| 作者 | Fu, Beide1,2; He, Shunping1 |
| 刊名 | DNA RESEARCH
 |
| 出版日期 | 2012-04-01 |
| 卷号 | 19期号:2页码:131-142 |
| 关键词 | silver carp transcriptome paired-end RNA sequencing |
| ISSN号 | 1340-2838 |
| 通讯作者 | He, SP (reprint author), Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, Wuhan 430072, Peoples R China. |
| 中文摘要 | 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. |
| 英文摘要 | 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. |
| WOS标题词 | Science & Technology ; Life Sciences & Biomedicine |
| 类目[WOS] | Genetics & Heredity |
| 研究领域[WOS] | Genetics & Heredity |
| 关键词[WOS] | TOXIC MICROCYSTIS BLOOMS ; CAJANUS-CAJAN L. ; SSR-MARKERS ; LAKE TAIHU ; IN-SITU ; GENOME ; ANNOTATION ; GENERATION ; REVEALS ; FISH |
| 收录类别 | SCI |
| 资助信息 | 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] |
| 语种 | 英语 |
| WOS记录号 | WOS:000303290100003 |
| 公开日期 | 2012-09-25 |
| 源URL | [http://ir.ihb.ac.cn/handle/342005/16809]  |
| 专题 | 水生生物研究所_水生生物多样性与资源保护研究中心_期刊论文 |
| 作者单位 | 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 |
| 推荐引用方式 GB/T 7714 | Fu, Beide,He, Shunping. 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.(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. |
入库方式： OAI收割
来源：水生生物研究所
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