title: Comparative analysis of microsatellites and compound microsatellites in T4-like viruses.
abstract: Microsatellites or simple sequence repeats (SSRs) are known to present ubiquitously in genomes of eukaryotes and prokaryotes, as well as viruses. A comprehensive analysis of microsatellites and compound microsatellites (CM) was performed for 67 T4-like bacteriophage genomes. We found that the number of repeats was generally proportional to the size of the genome. CM were more abundant in genic regions, while their relative abundance was higher in intergenic regions. Meanwhile, the number of CM rapidly decreased with the increase of complexity but gradually increased with higher dMAX (maximum distance between any two adjacent microsatellites). (A)n/(T)n, (AT)n/(TA)n and (AAG)n were the most abundant repeats of mono-, di- and trinucleotide microsatellites, respectively. The number of microsatellites in reference sequences was significantly lower than that in corresponding random sequences. This result was mainly attributed to mono- and dinucleotide repeats which hardly exceeded 6bp in T4-like viruses. These observations may be helpful to understand the distribution of microsatellites and viral genetic diversity in T4-like viruses.
authors.affiliation: College of Biology, Hunan University, Changsha 410082, China.
authors.forename: Lan
authors.initials: L
authors.lastname: Zhou
authors.affiliation: Department of General Surgery I, The Eastern Hospital of the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.
authors.forename: Liang
authors.initials: L
authors.lastname: Deng
authors.affiliation: College of Biology, Hunan University, Changsha 410082, China.
authors.forename: Yongzhuo
authors.initials: Y
authors.lastname: Fu
authors.affiliation: College of Biology, Hunan University, Changsha 410082, China.
authors.forename: Xiaolong
authors.initials: X
authors.lastname: Wu
authors.affiliation: College of Biology, Hunan University, Changsha 410082, China.
authors.forename: Xiangyan
authors.initials: X
authors.lastname: Zhao
authors.affiliation: Department of Computational Biology, Beijing Computing Center, Yongfeng Industry Base, Beijing 100094, China.
authors.forename: Yubao
authors.initials: Y
authors.lastname: Chen
authors.affiliation: Chinese Academy of Inspection and Quarantine, Beijing 100029, China.
authors.forename: Mingfu
authors.initials: M
authors.lastname: Li
authors.affiliation: College of Biology, Hunan University, Changsha 410082, China. Electronic address: zhongyang@hnu.edu.cn.
authors.forename: Zhongyang
authors.initials: Z
authors.lastname: Tan
mesh_terms: D017122:Bacteriophage T4 / Q000235:genetics*; D004279:DNA, Viral / Q000032:analysis; D014644:Genetic Variation; D059646:Genome Size; D018895:Microsatellite Repeats
chemical_list: D004279:DNA, Viral
keywords: Bacteriophages; Comparative genomics; Compound microsatellites; Microsatellites; T4-like viruses