Coevolution between simple sequence repeats (SSRs) and virus genome size

Abstract

BackgroundRelationship between the level of repetitiveness in genomic sequence and genome size has been investigated by making use of complete prokaryotic and eukaryotic genomes, but relevant studies have been rarely made in virus genomes.ResultsIn this study, a total of 257 viruses were examined, which cover 90% of genera. The results showed that simple sequence repeats (SSRs) is strongly, positively and significantly correlated with genome size. Certain repeat class is distributed in a certain range of genome sequence length. Mono-, di- and tri- repeats are widely distributed in all virus genomes, tetra- SSRs as a common component consist in genomes which more than 100 kb in size; in the range of genome < 100 kb, genomes containing penta- and hexa- SSRs are not more than 50%. Principal components analysis (PCA) indicated that dinucleotide repeat affects the differences of SSRs most strongly among virus genomes. Results showed that SSRs tend to accumulate in larger virus genomes; and the longer genome sequence, the longer repeat units.ConclusionsWe conducted this research standing on the height of the whole virus. We concluded that genome size is an important factor in affecting the occurrence of SSRs; hosts are also responsible for the variances of SSRs content to a certain degree.

Comparative analysis of microsatellites and compound microsatellites in T4-like viruses

“…However, this relationship does not exist in T4-like viruses. Our results indicate that the occurrence of microsatellites and CM is proportional to their genome sizes, similarly to what has been found in the vast majority of viral genomes (Zhao et al, 2012). In general, it is believed that the number of microsatellites or CM increases with genome size (Hancock et al, 2002).…”

“…Similarly, in other 257 viruses (which cover 90% of the genera), repeats with A/T bases are much more than those with G/C bases (Zhao et al, 2012). These results could be partially attributed to the high A/T content of the genomes (Karaoglu et al, 2005), as the A/T content in the analyzed sequences is only slightly higher than C/G content (Alam et al, 2013a).…”

“…A comparative analysis with other viruses indicated that microsatellite occurrence was similar to that of HIV-1 isolates(Chen et al, 2009;Chen et al, 2012), Hepatitis C virus (HCV)(Chen et al, 2011a), Potyvirus(Alam et al, 2013a;Zhao et al, 2012), Tobamovirus(Alam et al, 2013b), Human papillomavirus (HPV)(Singh et al, 2014), Carlavirus(Alam et al, 2014a) and Potexvirus(Alam et al, 2014b). Additionally, relative abundance and relative density of CM in T4-like viruses were lower than the above mentioned species.…”

“…Microsatellites, also known as simple sequence repeats (SSRs), are generally defined as simple sequences of 1-6 nucleotides that are repeated multiple times (Chen et al, 2009;Li et al, 2004;Zhao et al, 2012). Microsatellites have been found ubiquitously present but differentially distributed across the genomes of eukaryotes, prokaryotes and viruses; these sequences often exhibited variation in length with respect to the number of motifs being repeated.…”

The genome of herpes simplex virus type 1 is prone to form short repeat sequences

“…Long tandem repeats are observed to be hypermutable, but are rare in exons and only occasionally related with diseases in human [7,10]. However, STRs are extremely common and scattered in both coding and non-coding regions in eukaryote [11], prokaryote [12] and also viral [13] genomes. Why are the SSRs so common?…”