The analysis of microsatellites and compound microsatellites in 56 complete genomes of Herpesvirales |
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Authors: | Xiaolong Wu Lan Zhou Xiangyan Zhao Zhongyang Tan |
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Affiliation: | College of Biology, Hunan University, Changsha 410082, China |
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Abstract: | Simple sequence repeats (SSRs), or microsatellites, are special DNA/RNA sequences with repeated unit of 1–6 bp. The genomes of Herpesvirales have many repeating structures, which is an excellent system to study the evolution and roles of microsatellites and compound microsatellites in viruses. Therefore, 56 genomes of Herpesvirales were selected and the occurrence, composition and complexity of different repeats were investigated in the genomes. A total of 63,939 microsatellites and 5825 compound microsatellites were extracted from 56 genomes. It found that GC content has a significant strong correlation with both the counts of microsatellites (CM) and the counts of compound microsatellites (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 number of compound microsatellite decreases with the increase of complexity (C) (the count of individual microsatellites being part of a compound microsatellite) and the complexity hardly exceeds C = 4. The vast majority of compound microsatellites exist in intergenic regions, when C ≥ 10. The distributions of SSRs tend to be 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. |
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Keywords: | SSRs, simple sequence repeats cSSR, individual microsatellites being part of such a compound microsatellite CM, the counts of microsatellites in each genome CCM (also called CCMobs), the counts of compound microsatellites in each genome CCMexp, the expected counts of compound microsatellites in each genome CcSSR, the counts of cSSR in each genome cSSR%, the percentage of CcSSR account for CM in each genome (cSSR% = CcSSR/CM) RA, relative abundance. The number of microsatellites (or compound microsatellites) per kb RD, relative density. A total length (bp) contributed by each microsatellite (or compound microsatellite) per kb |
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