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Background  Ongoing molecular processes in a cell could target microsatellites, a kind of repetitive DNA, owing to length variations and motif imperfection. Mutational mechanisms underlying such kind of genetic variations have been extensively investigated in diverse organisms. However, obscure impact of ploidization, an evolutionary process of genome content duplication prevails mostly in plants, on non-coding DNA is poorly understood.    Results  Genome sequences of diversely originated plant species were examined for genome-wide motif imperfection pattern, and various analytical tools were employed to canvass characteristic relationships among repeat density, imperfection and length of microsatellites. Moreover, comparative genomics approach aided in exploration of microsatellites conservation footprints in  Gossypium  evolution. Based on our results, motif imperfection in repeat length was found intricately related to genomic abundance of imperfect microsatellites among 13 genomes. Microsatellite decay estimation depicted slower decay of long motif repeats which led to predominant abundance of 5-nt repeat motif in  Gossypium  species. Short motif repeats exhibited rapid decay through the evolution of  Gossypium  lineage ensuing drastic decrease of 2-nt repeats, of which, “AT” motif type dilapidated in cultivated tetraploids of cotton.    Conclusion  The outcome could be a directive to explore comparative evolutionary footprints of simple non-coding genetic elements i.e., repeat elements, through the evolution of genus-specific characteristics in cotton genomes.    Electronic supplementary material  The online version of this article (doi:10.1186/s41065-017-0034-4) contains supplementary material, which is available to authorized users.

A comparative genomics approach revealed evolutionary dynamics of microsatellite imperfection and conservation in genus Gossypium