Microsatellite dynamics across plant genomes an in silico study

Abstract

Microsatellites, also known as simple sequence repeats (SSRs), are short tandem repeat newlinesequences of 1-6 nucleotides that are ubiquitously and abundantly found in the genomes newlineof plant species. They are known to exhibit high levels of polymorphism, making them newlinevaluable molecular markers for studying genetic diversity, population dynamics, newlinegenome mapping and phylogenetics. The dynamic nature of microsatellites, including newlinetheir mutation rates, allelic variation, and distribution patterns, can provide valuable newlineinsights into the genomic dynamics of different plant species. This thesis focuses on newlineinvestigating the microsatellite dynamics in different plant genomes. Through a newlinecomprehensive analysis of the data available in the public domain, the thesis explores newlinethe patterns of microsatellite distribution, abundance, and variation in various plant newlinegenomes, and discusses the factors that contribute to their dynamic nature. The work newlinereported also highlights the role of microsatellites in relation to evolutionary dynamics newlinein plant species. We performed genome-wide searches across 144 plant genomes for newlinepotential microsatellite motifs from mono-, di-, tri-, tetra-, penta- and hexa-nucleotide. newlineA total of 38,309,047 microsatellites were identified in all the species with average newlinenumber of 2,66,035.04 microsatellites in genomic sequences. newlineLowest number of microsatellites was obtained in Lupinus angustifolius (10,079 newlinerepeats) having genome size of 609.203 Mb, whereas highest number of microsatellites newlinewas obtained in Triticum aestivum with 1,519,684 repeats in genome size of 14.547 Gb. newlineThe genome size of the species was in range from 119.67 Mb (Arabidospis thaliana) to newline14,547.26 Mb (Triticum aestivum). The total abundance was found 60524.97 in all plant newlinegenomes with an average of 420 microsatellites per Mb of genome. Least microsatellite newlineabundant genome was Lupinus angustifolius with only 16 microsatellites per Mb of its newlinegenome whereas highest abundance was found in Ficus carica with 1613.89 newlinemicrosatellites per Mb of genome...