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

• 作 者: KONG Jie GAO Huan
• 机 构: Key Laboratory for Sustainable Utilization of Marine Fisheries Resources,Institute of Oceanology,The
• 出 处: 科学通报（英文版）
• 发表日期: 2004年期
• 关键词: tandem repeats microsatellites minisatellites Fenneropenaeus chinensis genome
• 基金项目: National Basic Research Priorities Programme (973);National High-Tech Research and Development Program of China (863);Open-end Funds of Key Laboratory of Fisheris Genetic Resources & Aquaculture;Chine

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.