Consensus features of microsatellite distribution: Microsatellite contents are universally correlated with recombination rates and are preferentially depressed by centromeres in multicellular eukaryotic genomes

Microsatellite DNA is highly polymorphic and informative, which makes its distribution pattern and its associations very valuable for marker applications and genomic research in evolution. Using computational and statistical approaches, based on database technology, we have demonstrated that microsatellite content is consistently and significantly 2 to 5 fold lower than the average chromosomal level in the centromeric and pericentromeric regions of the chromosomes of two plant species, Arabidopsis thaliana and Oryza sativa. We conducted a path coefficient analysis to compare the direct effect of microsatellites (from mono-nucleotide through to penta-nucleotide repeats) on recombination rates. The results revealed that tri- and penta-nucleotide microsatellites significantly influence recombination rates. In the human genome, tri-, tetra- and mono-nucleotide microsatellites, in decreasing order, make significant direct contributions to recombination rates, according to DECODE, GENTHON, and MARSHFIELD averages. Path coefficient analysis in rice and human genomes of the impact of di-nucleotide microsatellites of different motifs on recombination rates indicate that motifs with either A or T have an effect, resulting in increased recombination rates for microsatellites with motifs consisting of 50% A or T, such as AG, TC, CA, TG. Conversely, microsatellites with motifs consisting of only A & T or G & C, such as AT, TA, GC or CG, have decreased recombination rates. The extremely low microsatellite content in centromeric and pericentromeric regions, as well as the quantitative association of microsatellite sequences with the recombination rate at the genome level, suggests that purifying selection in genome evolution creates a balance between genomic polymorphisms and the biological function of sequences in a genome.