Occurrence And Distribution Analysis Of Microsatellites In Bacteriophages Genomes

A large number of repetitive sequences were found in the non-coding sequences after completion of human genome project (HGP). Nowadays, an increasing number of studies show that the repetitive sequence is an important part of the genome, which is involved in the expression of genes and the growth or development of organisms. As a relatively simple kind of repetitive sequences, microsatellite draw attention as associated with a variety of human nervous system diseases, and then it has been used in many fields of molecular biology research. Study on microsatellite mainly focus in eukaryotes and prokaryotes, it began to relate to viruses in recent years. Bacteriophage is a kind of ancient bacterial virus with abundant quantity, which is one of the model organisms of biomedical research, they have been widely used in the treatment of some diseases caused by bacteria and does not cause harm to human normal cells. In this paper, we use the sequence information existed in the database, by means of biology, statistics and computer technology, to analyze microsatellite occurrence in Bacteriophages. Our research may provide theoretical support for understanding the evolution process and pathogenesis of the viruses.This paper mainly involves the following two aspects:1. Comparative analysis of microsatellites and compound microsatellites in T4-like viruses (Chapter 2)In this chapter, we selected 67 sequences of T4-like viruses which belongs to Caudovirales, and analyzed the occurrence and distribution patterns of microsatellites and compound microsatellites. Results showed that the relative abundance (RA) and relative density (RD) of microsatellites have no significant difference with smaller genomes of animal and plant viruses, while compound microsatellites was slightly lower than several viruses compared. To further evaluate whether the occurrence of microsatellite is randomly in T4-like viruses, a random model written in C programming language was used to produce 67 random sequences. The base composition and genome size in each random sequence is equal to corresponding reference sequence. Results showed that the incidence of microsatellites was significantly lower than corresponding random sequences, but reference sequences have a specific preference for trinucleotide repeats. Pearson linear correlation analysis showed that there was a significant positive correlation between genome size and the incidence of microsatellites and compound microsatellites. Genomic GC content was slightly lower than that of AT content, but A/T content accounts for the most part in repetitive sequences, this may attributed to that A/T gathered together is relatively easy to form a hairpin structure to regulate the expression of genetic information. The number of compound microsatellites rapidly decreased with the increase of complexity but gradually increased with higher dMAX (maximum distance between any two adjacent microsatellites). Although genie regions are relatively longer in T4-ike viruses, RA showed that more compound microsatellites appeared in intergenic regions with low conservation. The study of repetitive sequences will help us to better understand the genetic diversity and biological evolution of T4-ike viruses.2.Differential analysis of microsatellites between bacteriophages and herpesviruses (Chapter 3)In Chapter 2, we found that microsatellite occurrence in T4-like viruses was significantly lower than corresponding random sequences. By consulting the literatures, it is found that the genome of herpesvirus is also very large, and the similarity in capsid protein structure showed that the two viruses originated very close, they may have a common ancestor. Therefore, we selected 46 genomic sequences from both Caudovirales and Herpesviruses, respectively. These sequences were numbered by genome length and corresponding sequences have similar length. Results showed that the incidence of microsatellites in bacteriophages was significantly lower than corresponding herpesviruses. Curve fitting analysis showed that GC content can influence the occurrence of the microsatellites in the same species, and the high or low GC content can greatly increased the occurrence of repetitive sequences. In different species, the microsatellite content in herpesviruses is twice as high as that in bacteriophages with the same GC content. Further analysis showed that the difference was mainly from the sequence itself. Herpesviruses may have co-evolution with their hosts, as their internal repeat and terminal repeat regions have numerous repetitive sequences, which are similar to centriole and telomere structure in eukaryotes. In addition, we found that GC content has a convergence trend in bacteriophages and their hosts, which provides evidences to further prove the co-evolution between th bacteriophages and their hosts. Microsatellite analysis indicates that organisms with the same origin would evolve in different directions, this may attributed to that they selected different hosts in the process of evolution and the existence of co-evolution with their hosts. These analyses may provide help for further study of the evolution of viruses.