Survey And Analysis Of Simple Sequence Repeats In Viroid And Mononucleoitde Repeat In Virus Genomes

Simple sequence repeats (SSR), also known as microsatellites, comprise tandemly repeated genetic loci of one to six base pairs. The functional importance of these sequences is well-known and they commonly form the focus of genome analysis. Until now, extensive simple sequence repeat (SSR) surveys have been performed for eukaryotic, prokaryotic and viral genomes, but information regarding SSR in viroids and viruses is limited. In this study, we analyzed the simple sequence repeats loci in some viroid and virus genomes and get some conclusions. Furthermore, we discussed the SSR distribution and predicted the potential reason and its function in the genomes, which could be helpful for our deep understanding of genome evolution, diversity and viroid taxonomy.Survey and analysis of simple sequence repeats (SSR) present in the genomes of plant viroids. The results of this investigation showed that viroid genomes contain a relatively high percentage of SSR in comparison with random sequences. Moreover, by comparing the polymorphism of SSR loci in97PSTVd genomes and analyzing the distribution of SSR loci in five domain, our results indicated that the distribution of SSR in viroids influences secondary structure, and that SSR may play a role in generating genetic diversity. We also examined the potential evolutionary role of repeated sequences in the viroid genome. This is the first report of SSR loci in viroids and our study could be helpful in understanding the structure and evolution of viroid genomes.Survey and analysis of mononucleotide repeat (SSR) present in the genomes of virus. Mononucleotide repeats (MNR) also known as homopolymeric tracts, are an important type of SSR, consisting of a repeated sequences of a single nucleotide. In this study, we examined the distribution of MNRs in256fully sequenced virus genomes. Our results showed extensive variation in the distribution of MNR in viral genomes, and indicated that this is significantly influenced by both genome size and CG content. Furthermore, the ratio of the observed to the expected number of MNR (O/E ratio) appears to be influenced by both the host range and genome type of a particular virus. Additionally, the densities and frequencies of MNR in genic regions are lower than those in non-coding regions, which suggests that selective pressure acts on viral genomes. We also examined the potential functional roles of these MNR loci in virus genomes. To our knowledge, this is the first analysis of MNR in viruses, and our study could have potential implications for a deeper understanding of virus genome stability and the co-evolution that occurs between a virus and its host.