Survey and analysis of simple sequence repeats (SSRs) present in the genomes of plant viroids

• We 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.

Extensive simple sequence repeat (SSR) surveys have been performed for eukaryotic prokaryotic and viral genomes, but information regarding SSRs in viroids is limited. We undertook a survey to examine the presence of SSRs in viroid genomes. Our results show that the distribution of SSRs in viroids may influence secondary structure, and that SSRs could play a role in generating genetic diversity. We also discuss 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.