| Existence of Microsatellites in Expressed Sequence Tags of Common Carp （Cyprinus carpio L. ） Available in GenBank dbEST Database |
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| 作者姓名： | HU Jingjie WANG Xiaolong HU Xiaoli BAO Zhenmin |
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| 作者单位： | Laboratory of Marine Genetics and Breeding, Division of Life Science and Biotechnology,Ocean University of China, Qingdao 266003, P. R. China |
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| 基金项目： | 教育部海洋生物重点实验室基金 |
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| 摘 要： | Common carp expressed sequence tags （ESTs） were analyzed for the existence of microsatellites, or simple sequence repeats （SSRs）. In the NCBI dbEST database, a total of 10612 sequences were registered before December 31, 2004. A complete search of 2-6 nucleotide microsatellites resulted in the identification of 513 SSR-containing ESTs, accounting for 4.8% of the total. Cluster analysis indicated that 73 sequences of SSR-containing ESTs fell into 27 groups and the remaining 440 ESTs were independent. A total of 467 unique SSR-containing ESTs were identified. These EST-SSRs contained a vari- ety of simple sequence types, and di- and tri-nucleotide repeats were the most abundant, accounting for 42.1% and 27.9% of the whole, respectively. Of the dinucleotide repeats, CA/TG was the most abundant, followed by GA/TC. BLASTx search showed that 38.1% of the SSR loci could be associated with genes or proteins of known or unknown function. BLASTx searches of SSR-containing ESTs also showed high frequencies （98/179） of hits on zebrafish sequences.
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| 关 键 词： | 鲤鱼 序列标签 淡水鱼 数字渔业 |
| 收稿时间： | 2005-04-13 |
| 修稿时间： | 2005-12-06 |
Existence of microsatellites in expressed sequence tags of common carp (Cyprinus carpio L.) available in GenBank dbEST database |
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| HU Jingjie WANG Xiaolong HU Xiaoli BAO Zhenmin.Existence of microsatellites in expressed sequence tags of common carp (Cyprinus carpio L.) available in GenBank dbEST database[J].Journal of Ocean University of China,2006,5(1):12-20. |
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| Authors: | Hu Jingjie Wang Xiaolong Hu Xiaoli Bao Zhenmin |
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| Institution: | Laboratory of Marine Genetics and Breeding, Division of Life Science and Biotechnology, Ocean University of China, Qingdao 266003, P .R .China |
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| Abstract: | Common carp expressed sequence tags (ESTs) were analyzed for the existence of microsatellites, or simple sequence repeats (SSRs). In the NCBI dbEST database, a total of 10612 sequences were registered before December 31, 2004. A complete search of 2-6 nucleotide microsatellites resulted in the identification of 513 SSR-containing ESTs, accounting for 4.8% of the total. Cluster analysis indicated that 73 sequences of SSR-containing ESTs fell into 27 groups and the remaining 440 ESTs were independent. A total of 467 unique SSR-containing ESTs were identified. These EST-SSRs contained a variety of simple sequence types, and di- and tri-nucleotide repeats were the most abundant, accounting for 42.1% and 27.9% of the whole, respectively. Of the dinucleotide repeats, CA/TG was the most abundant, followed by GA/TC.BLASTx search showed that 38.1% of the SSR loci could be associated with genes or proteins of known or unknown function. BLASTx searches of SSR-containing ESTs also showed high frequencies (98/179) of hits on zebrafish sequences. |
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| Keywords: | common carp microsatellites ESTs data mining |
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