Analysis on Frequency and Density of Microsatellites in Coding Seauences of Several Eukarvotic Genomes  

作　　者：BinLi QingyouXia ChengLu ZeyangZhou ZhonghuaiXiang 

机构地区：[1]TheKeySericulturalLaboratoryofAgriculturalMinistry,CollegeofSericultureandBiotechnology,SouthwestAgriculturalUniversity,Chongqing400716,China

出　　处：《Genomics, Proteomics & Bioinformatics》2004年第1期24-31,共8页基因组蛋白质组与生物信息学报（英文版）

基　　金：This work was supported by the Hi-Tech Research and Development Program of China (863 Program) and the National Natural Science Foundation of China (No. 30300262).

摘　　要：Microsatellites or simple sequence repeats (SSRs) have been found in mostorganisms during the last decade. Since large-scale sequences are being generated, especially thosethat can be used to search for microsatellites, the development of these markers is getting moreconvenient. Keeping SSRs in viewing the importance of the application, available CDS (codingsequences) or ESTs (expressed sequence tags) of some eukaryotic species were used to study thefrequency and density of various types of microsatellites. On the basis of surveying CDS or ESTsequences amounting to 66.6 Mb in silkworm, 37.2 Mb in fly, 20.8 Mb in mosquito, 60.0 Mb in mouse,34.9 Mb in zebrafish and 33.5 Mb in Caenorhabditis elegans, the frequency of SSRs was 1/1.00 Kb insilkworm, 1/0.77 Kb in fly, 1/1.03 Kb in mosquito, 1/1.21 Kb in mouse, 1/1.25 Kb in zebrafish and1/1.38 Kb in C. elegans. The overall average SSR frequency of these species is 1/1.07 Kb.Hexanucleotide repeats (64.5%—76.6%) are the most abundant class of SSR in the investigatedspecies, 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 thecoding regions.Microsatellites or simple sequence repeats (SSRs) have been found in mostorganisms during the last decade. Since large-scale sequences are being generated, especially thosethat can be used to search for microsatellites, the development of these markers is getting moreconvenient. Keeping SSRs in viewing the importance of the application, available CDS (codingsequences) or ESTs (expressed sequence tags) of some eukaryotic species were used to study thefrequency and density of various types of microsatellites. On the basis of surveying CDS or ESTsequences amounting to 66.6 Mb in silkworm, 37.2 Mb in fly, 20.8 Mb in mosquito, 60.0 Mb in mouse,34.9 Mb in zebrafish and 33.5 Mb in Caenorhabditis elegans, the frequency of SSRs was 1/1.00 Kb insilkworm, 1/0.77 Kb in fly, 1/1.03 Kb in mosquito, 1/1.21 Kb in mouse, 1/1.25 Kb in zebrafish and1/1.38 Kb in C. elegans. The overall average SSR frequency of these species is 1/1.07 Kb.Hexanucleotide repeats (64.5%—76.6%) are the most abundant class of SSR in the investigatedspecies, 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 thecoding regions.

关 键 词：INSECT EUKARYOTE CDS EST MICROSATELLITE 

分 类 号：Q74[生物学—分子生物学]