Microsatellites (SSRs): Puzzles within puzzle

Abstract

SSRs are not only found in all genomes (big or small) Mycoplasma vs animals but also in the smallest and compact genome amongst vertebrates like fish and birds. These findings suggest that microsatellites cannot be totally eliminated from the genome. Studies on distribution, frequency and pattern of SSRs in coding and non-coding regions reveal species specific, length or pattern dependent features, which suggest that SSRs are common in intergenic regions of all organisms. CG dinucleotide repeats are scarce and trinucleotide tolerance is more in the coding sequences. However, there are features about microsatellites, which may not fall in any paradigm, as what may be true regarding motifs in one organism may not be so for others. This is evident from the studies that show rarity of (GT)n repeat in plants vis-a-vis mammals which have these repeats in abundance. Similarly, abundance of AAT repeats is found in introns of most organisms but rodents are exceptional in having AAG abundance. To highlight these features and to address the question regarding microsatellite abundance in relation to increasing genomic complexity, data from various sources have been tabulated for this review. Different schools of thought about the origin and evolution of microsatellites are also discussed.