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

文献类型： 外文期刊

作者： Kong, J 1 ; Gao, HA 2 ;

作者机构： 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 Fishery Sci, Yellow Sea Fisheries Res Inst, Minist Agr, Key Lab Sustainable Utilizat Maraine Fisheries Re, Qingdao 266071, Peoples R China; Chinese Acad Sci, Inst Oceanol, Qingdao 266071, Peoples R China; Chinese Acad Sci, Grad Sch, Beijing 100039, Peoples R China

关键词： tandem repeats;microsatellites;minisatellites;Fenneropenaeus chinensis;genome

期刊名称：CHINESE SCIENCE BULLETIN （ 影响因子：1.649； 五年影响因子：1.738 ）

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收录情况： SCI

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 percent and 20.6 percent of repeat sequences, respectively. The cumulative length of repeat sequences was found to be 116685 bp, accounting for 13.2 percent of the total DMA sequence; the cumulative length of microsatellites occupied 9.78 percent of the total DMA sequence, and that of minisatellites occupied 3.42 percent. ib 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.

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