Occurrence and Analysis of Microsatellites and Compound Microsatellites in Caudovirales

doi:10.13523/j.cb.20141104

China Biotechnology

2014, Vol. 34

Issue (11): 24-33 DOI: 10.13523/j.cb.20141104

Occurrence and Analysis of Microsatellites and Compound Microsatellites in Caudovirales

ZHOU Lan¹, WU Xiao-long¹, FU Yong-zhuo¹, ZHAO Xiang-yan¹, CHEN Yu-bao², TAN Zhong-yang¹

1. College of Biology, Hunan University, Changsha 410082, China;
2. Department of Computational Biology, Beijing Computing Center, Yongfeng Industry Base, Beijing 100094, China

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Abstract

Simple sequence repeats (SSRs) or microsatellites have been successfully used for various genetic and evolutionary studies in eukaryotic, prokaryotic and viral systems, but information regarding SSRs in bacteriophages is limited by lack of studies. We made a comprehensive analysis of microsatellites and compound microsatellites (composed of two or more microsatellites residing directly adjacent to each other) in 60 Caudovirales genomes, and a total of 11 874 microsatellites and 449 compound microsatellites were observed in these genomes. In general, the count of SSRs is proportional to genome size by Pearson linear correlation analysis (ρ=0.899,P<0.01). Microsatellites in reference sequences are lower than that in random sequences, and it was beyond our expectation. The primarily reason was that reference sequences contain fewer mononucleotide and dinucleotide repeats. A/T and AT/TA were predominant in mononucleotide and dinucleotide repeats in most sequences, so GC content in mononucleotide repeats was notably lower than that in corresponding genome; by contrast, GC content has no significant difference between reference sequences and microsatellites of dinucletide and trinucleotide repeats. These results in Caudovirales are more or less different from other organisms' genomes. Our study might be helpful in understanding the distribution, evolution and biological function of microsatellites in Caudovirales.

Key words： Microsatellite Compound microsatellite Bacteriophage Caudovirales Distribution

Received: 20 September 2014 Published: 25 November 2014

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ZHOU Lan, WU Xiao-long, FU Yong-zhuo, ZHAO Xiang-yan, CHEN Yu-bao, TAN Zhong-yang. Occurrence and Analysis of Microsatellites and Compound Microsatellites in Caudovirales. China Biotechnology, 2014, 34(11): 24-33.

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https://manu60.magtech.com.cn/biotech/10.13523/j.cb.20141104 OR https://manu60.magtech.com.cn/biotech/Y2014/V34/I11/24

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