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.

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HighlightsWe identified simple sequence repeats (SSRs) of 1–6 nt in 36 reference viroid genomes.Compared to randomly generated sequences, SSRs are over-represented in viroid genomes.Relative SSR content ranged from 4.72% to 31.89%, averaging 18% of the viroid genome.SSRs in viroids might influence secondary structure and contribute to genetic diversity.We hypothesize that SSRs might drive the evolution of viroid genomes.