Primary Research On The Microsatellite Distribution And Function In Genomes And The Relevant Computational Methodology

Microsatellite is the tandemly repeated fragment in genomic sequences, composed of 1-6 base pairs in length, so microsatellite also called Short Tandem Repeat (SIR) or Simple Repeat Sequence (SSR). Microsatellites in genomic sequences are ubiquitously polymorphic, they are broadly applied to population genetic variation analysis, the research on origin and evolution of organisms, genotyping, fingerprinting, forensic science, animal and plant breeding etc. So the analysis of microsatellites about the content, distribution and associations in genomes would provide significant prior information towards microsatellite application, avoiding the scrambles of experimental science. To date with the increase of databases of sequences, the investigation will obtain more precise and novel conclusion.Using Perl as programming language and integrating databases technology, microsatellites, longer than 12 nucleotides in length, in 29 eukaryotic and 1180 prokaryotic genomes were computed and censused in great scale. The following items were studied: microsatellite distribution on chromosomes, the relationship between microsatellite content and genetic recombination rate in genomic scale, the microsatellite distribution of commonness and individuality in the eukaryotic and prokaryotic genomes, the associations between the polymorphisms in computation and in experiment, the characteristics of microsatellite distribution in orphan and non-orphan genes. The investigation would provide the feasible theories and fundamentals of microsatellite application with significance. Meanwhile the study also explored the bioinformatic computation method in local and remote WEB computation through Internet. The major results showed as follows:1. Microsatellite distribution on chromosomes showed: microsatellite content in centromeric and pericentromeric regions is notably lower than in others and generally higher in distal regions. Even in acrocentromeric region, the microsatellite content is still lower than chromosomalaverage, the phenomena expresses the priority of centromere in conservation. The consistent conclusion was confirmed by the computation and statistics of microsatellites in the sequences in Arabidopsis thaliana, Oryza sativa and Homo sapiens genomes, nevertheless the rule could not be concluded in the unicellular prokaryotes such as Schizosaccharomyces pombe.2. The relationship coefficients between microsatellite content among the closest markers and the recombination rate among the above markers were computed in human and rice genomes. The computation showed the RS statistic of Spearman rank correlation coefficient obtained from the data pairs is 0. 3217 with 2725 in sample size in rice (cultivar Nipponbare) genome, while the 2-tailed deniable probability equals to zero, and the same kind of RS statistic, which equals to 0. 1111 with 2759 in sample size and the 2-tailed deniable probability also equals3. 9045X10-9, was observed in human genome.3. The computation and census of microsatellites in 29 eukaryotic and 1180 prokaryotic genomes showed: (1) microsatellite content in eukaryotes is generally higher than in prokaryotes, but with a lot of exceptions; (2) the variation coefficient of microsatellite content in eukaryotes is not so high, which is 75% in 29 eukaryotes, while that in prokaryotes with represent of viruses reaches 91%. So we speculated that the prokaryotes are the microsatellite-cumulative species, while the eukaryotes are the microsatellite-content-stable ones; (3) the total motif number in prokaryotes is lower and that in eukaryotes is higher. Nonetheless the microsatellite content in some species in prokaryotes is higher than in eukaryotes, the microsatellites are only deposited in local in genomic sequences but the motif number is consistently low. (4) That the positive relationship coefficients between the number of microsatellite motif and genome size in both eukaryotic and prokaryotic genomes were significant, was found. The relationship coefficient between microsatellite content and the genome size w...