The genome of herpes simplex virus type 1 is prone to form short repeat sequences

Xiangyan Zhao, Xiaolong Wu, Lv Qin, Zhongyang Tan, Shifang Li, Qingjian Ouyang, You Tian

College of Biology, State Key Laboratory for Chemo/Biosensing and Chemometrics, Hunan University, Changsha, China.
State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.

DOI: 10.4236/jbm.2013.13006                

Abstract

Herein, we report a very high content of simple sequence repeats (SSRs) covering 66.12% of the herpes simplex virus type 1 (HSV-1) genome when a low threshold is adopted to define SSRs, indicating that repeat sequence is a very important character of the HSV-1 genome. The repeats with two iterations account for 68.33% of the total repeats. In reality, the genome of HSV-1 is prone to form shorter repeat sequences. For mono-, di- and trinucleotide repeats, the repeat numbers decreased with the increase of repeats iterations, implicating that the formation tendency of SSRs might be from low iterations to high iterations. The high iterations SSRs might have subjected to strong selected pressure and survived to perform different functions. The analysis suggested that the repeats formation may be an essential evolutionary driving force for the HSV-1 genome, and the results might be helpful for studying the genome structure, repeats genesis and genome evolution of HSV-1.

Keywords

Simple Sequence Repeat; HSV-1 Genome; Microsatellite; SSR

Conflicts of Interest

The authors declare no conflicts of interest.

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