Comparative genomics analysis gives insights into differential microsatellite distribution in selected cereals and legumes

The sequencing revolution for plant genomes generated a large amount of data that could be utilized for studying plant variations and evolution. Microsatellites are a potential source of quantitative genetic variation in the evolution of complex plant genomes in response to changing environmental cues. Therefore, investigating the microsatellite variations in the plant genome will provide the cues for crop improvement. The present investigation collected genomic and coding sequence information for six monocot cereals (finger millet, rice, sorghum, maize, foxtail millet, and wheat) and six dicot legumes (Arabidopsis, Medicago, soybean, chickpea, cowpea, and common bean) to examine genome-wide comparative analysis of microsatellite distribution. The Perl script MIcroSAtellite (MISA) was used for in silico mining of microsatellites. The relative abundance of microsatellites in the genome of dicots (451.26/Mb) was significantly higher than in monocots (204.92/Mb). In contrast, monocots have a higher relative abundance of microsatellites (144.45/Mb) at coding regions than dicots (67.52/Mb). It is also revealed that GC-rich motifs are more abundant in genomic and coding sequences of monocot plant species compared to dicots, where AG-rich motifs are more prevalent in dicots. The tri-nucleotide repeats were predominant over any other repeat types in the coding region of both monocot and dicot plant species. This study portrays the dynamics of differential microsatellite distribution in genomic and coding sequences of both monocots and dicots, providing valuable insight into the origin of microsatellites during the divergence of monocots and dicots.