| Microsatellites, or Simple sequence repeats(SSRs), are special DNA/RNA sequences with repeated unit of 1-6 bp. However, both experimental and computational biology research on microsatellites were mainly aimed at the genomes of eukaryotes and prokaryotes. Virus is a microscopic particles, cannot survive in the natural environment, parasitizing in the living cells. By far, reports related to viral microsatellite researches were rare, and primarily focused on the viruses with short genomes(less than 10 kbp), that is to say, the distribution and composition of microsatellites have not been analyzed in the virus with long genomes(more than 100 kbp). The genomes of herpesvirus have many repeating structures and genome size ranged from 125 to 295 kbp, which is an excellent system to study the evolution and function of microsatellites. Therefore, in this dissertation, the 56 available genomes of Herpesvirales were selected and the occurrence, composition and complexity of different repeats were investigated and analyzed in the genomes, by means of mathematics, statistics and computer technology. Additionally, we discussed the possible roles the microsatellites playing in the origination and evolution of herpesvirales genomes.This dissertation has mainly completed the following work:All microsatellites and compound microsatellites were extracted from 56 genomes by perl language; the genome size, GC content, the counts of microsatellites(CM), the counts of compound microsatellites(CCM), relative abundance(RA), relative density(RD) were calculated and analyzed in this chapter. we found that GC content has a significant strong correlation with both CM and CCM. However, genome size has a moderate correlation only with CM and almost no correlation with CCM. The compound microsatellites occurring in genic regions are obviously more than that in intergenic regions. In general, the CCM decreases with the increasing of complexity(C)(the count of individual microsatellites being part of a compound microsatellite), which hardly exceeds C=4. The vast majority of compound microsatellites exist in intergenic regions, when C ?10. The distributions of SSRs tend to organism-specific rather than host-specific in herpesvirus genomes. The diversity of microsatellites and compound microsatellites may be helpful for a better understanding of the viral genetic diversity, genotyping, and evolutionary biology in herpesviruses genomes.In order to estimate the differences of SSRs between reality and random, a random model written in perl language was designed to generate 56 random sequences, whose number of adenine, thymine, guanine and cytosine are same to corresponding reference sequences downloaded from the database. In this work, RD of microsatellites was calculated and analyzed in 56 Herpesvirales genomes and random sequences. The results showed that t he number of units, unit size and GC content are important factors in affecting the formation of microsatellites. Compared to random sequences, the RD significantly increased 5.5 percent in genomes. The 5.5% expansion of SSRs can attribute to each region o f a herpesviruses genome, especially in internal repeat(IR) and terminal repeat(TR). Some genomic structural similarities are found between herpesviruses and vertebrate. The conservative sequences(TTAGGG)n might indicate that there are some relationships between vertebrate and herpesviruses in origin. The 6 genomes of Simplexvirus were selected as material and the analysis of genome-wide comparison was done. The results revealed that: high homology mainly existed in the region of unique long(UL) and unique short(US) which covered more than 90% genes; the low homologous regions are in the regions of IR and terminal repeat TR; the RL1, RL2, RS1 and UL36 gene with low homology in the regions of TR/IR might be the reason of difference in first step of infection. The analysis may be helpful for further studying the roles of microsatelli tes in genome origination and evolution of Herpesvirales. |
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