Analysis on Frequency and Density of Microsatellites in Coding Sequences of Several Eukaryotic Genomes

Microsatellites or simple sequence repeats (SSRs) have been found in most organisms during the last decade. Since large-scale sequences are being generated, especially those that can be used to search for microsatellites, the development of these markers is getting more convenient. Keeping SSRs in viewing the importance of the application, available CDS (coding sequences) or ESTs (expressed sequence tags) of some eukaryotic species were used to study the frequency and density of various types of microsatellites. On the basis of surveying CDS or EST sequences amounting to 66.6Mb in silkworm, 37.2Mb in fly, 20.8Mb in mosquito, 60.0Mb in mouse, 34.9Mb in zebrafish and 33.5Mb in Caenorhabditis elegans, the frequency of SSRs was 1/1.00Kb in silkworm, 1/0.77Kb in fly, 1/1.03Kb in mosquito, 1/1.21Kb in mouse, 1/1.25Kb in zebrafish and 1/1.38Kb in C. elegans. The overall average SSR frequency of these species is 1/1.07Kb. Hexanucleotide repeats (64.5%–76.6%) are the most abundant class of SSR in the investigated species, followed by trimeric, dimeric, tetrameric, monomeric and pentameric repeats. Furthermore, the A-rich repeats are predominant in each type of SSRs, whereas G-rich repeats are rare in the coding regions