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Analysis of tandem repeats in the genome of Chinese shrimp Fenneropenaeus chinensis

文献类型：期刊论文

作者Kong, J; Gao, HA
刊名CHINESE SCIENCE BULLETIN
出版日期2005-07-01
卷号50期号:14页码:1462-1469
关键词Tandem Repeats Microsatellites Minisatellites Fenneropenaeus Chinensis Genome
ISSN号1001-6538
DOI10.1360/982005-270
文献子类Article
英文摘要Through random sequencing, we found a total of 884000 base-pairs (bp) of random genomic sequences in the genome of Chinese shrimp (Fenneropenaeus chinensis). Using bio-soft Tandem Repeat Finder (TRF) software, 2159 tandem repeats were found, in which there were 1714 microsatellites and 445 minisatellites, accounting for 79.4% and 20.6% of repeat sequences, respectively. The cumulative length of repeat sequences was found to be 116685 bp, accounting for 13.2% of the total DNA sequence; the cumulative length of microsatellites occupied 9.78% of the total DNA sequence, and that of minisatellites occupied 3.42%. In decreasing order, the 20 most abundant repeat sequence classes were as follows: AT (557), AC (471), AG (274), AAT (92), A (56), AAG (28), ATC (27), ATAG (27), AGG (18), ACT (15), C (11), AAC (11), ACAT (11), CAGA (10), AGAA (9), AGGG (7), CAAA (7), CGCA (6), ATAA (6), AGAGAA (6). Dinucleotide repeats, not only in the aspect of the number, but also in cumulative length, were the preponderant repeat type. There were few classes and low copy numbers of repeat units of the pentanucleotide repeat type, which included only three classes: AGAGA, GAGGC and AAAGA. The classes and copy numbers of heptanucleotide, eleven-nucleotide and thirteen-nucleotide primer-number-composed repeats were distinctly less than that of repeat types beside them.; Through random sequencing, we found a total of 884000 base-pairs (bp) of random genomic sequences in the genome of Chinese shrimp (Fenneropenaeus chinensis). Using bio-soft Tandem Repeat Finder (TRF) software, 2159 tandem repeats were found, in which there were 1714 microsatellites and 445 minisatellites, accounting for 79.4% and 20.6% of repeat sequences, respectively. The cumulative length of repeat sequences was found to be 116685 bp, accounting for 13.2% of the total DNA sequence; the cumulative length of microsatellites occupied 9.78% of the total DNA sequence, and that of minisatellites occupied 3.42%. In decreasing order, the 20 most abundant repeat sequence classes were as follows: AT (557), AC (471), AG (274), AAT (92), A (56), AAG (28), ATC (27), ATAG (27), AGG (18), ACT (15), C (11), AAC (11), ACAT (11), CAGA (10), AGAA (9), AGGG (7), CAAA (7), CGCA (6), ATAA (6), AGAGAA (6). Dinucleotide repeats, not only in the aspect of the number, but also in cumulative length, were the preponderant repeat type. There were few classes and low copy numbers of repeat units of the pentanucleotide repeat type, which included only three classes: AGAGA, GAGGC and AAAGA. The classes and copy numbers of heptanucleotide, eleven-nucleotide and thirteen-nucleotide primer-number-composed repeats were distinctly less than that of repeat types beside them.
学科主题Multidisciplinary Sciences
URL标识查看原文
语种英语
WOS记录号WOS:000232195600011
公开日期2010-12-22
源URL[http://ir.qdio.ac.cn/handle/337002/3097]  
专题海洋研究所_实验海洋生物学重点实验室
作者单位1.Chinese Acad Fishery Sci, Yellow Sea Fisheries Res Inst, Minist Agr, Key Lab Sustainable Utilizat Maraine Fisheries Re, Qingdao 266071, Peoples R China
2.Chinese Acad Sci, Inst Oceanol, Qingdao 266071, Peoples R China
3.Chinese Acad Sci, Grad Sch, Beijing 100039, Peoples R China
推荐引用方式
GB/T 7714		 Kong, J,Gao, HA. Analysis of tandem repeats in the genome of Chinese shrimp Fenneropenaeus chinensis[J]. CHINESE SCIENCE BULLETIN,2005,50(14):1462-1469.
APA Kong, J,&Gao, HA.(2005).Analysis of tandem repeats in the genome of Chinese shrimp Fenneropenaeus chinensis.CHINESE SCIENCE BULLETIN,50(14),1462-1469.
MLA Kong, J,et al."Analysis of tandem repeats in the genome of Chinese shrimp Fenneropenaeus chinensis".CHINESE SCIENCE BULLETIN 50.14(2005):1462-1469.

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来源：海洋研究所

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