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

doi:10.1360/982005-270

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	Analysis of tandem repeats in the genome of Chinese shrimp Fenneropenaeus chinensis
	Kong, J ; Gao, HA
	2005-07-01
发表期刊	CHINESE SCIENCE BULLETIN
ISSN	1001-6538
卷号	50 期号:14 页码:1462-1469
文章类型	Article
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.
关键词	Tandem Repeats Microsatellites Minisatellites Fenneropenaeus Chinensis Genome
学科领域	Multidisciplinary Sciences
DOI	10.1360/982005-270
URL	查看原文
收录类别	SCI
语种	英语
WOS记录号	WOS:000232195600011
引用统计	被引频次：10[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.qdio.ac.cn/handle/337002/3096
专题	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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