| Genetic divergence spread widely in all lifes in the world. According to the classical model, most molecular divergence is result from genetic drift, genetic isolation and nature selection. Based on the genetic model, genetic divergence distributed in the populations in some regular pattern. Different frequency of genetic difference has regular relationship among them.To test the regular of frequency distribution of genetic divergence between individuals in molecular, many studies focus on polymorphisms of functional genes or genome wide regions in Arabidopsis thaliana, and the result show an excess of rare alleles. The inconformity between expectation and results imply that we need new thinking and method. It is important to study the frequency variation of genetic divergence and mechanism of generation and evolution. Therefore, we do a detail study on the number, characters, distribution and pattern of gene evolution in Arabidopsis thaliana.Therefore, we used an outgroup sequence to characterize rare alleles of 939 loci in 96 Arabidopsis accessions to distinguish characters of SNPs and low-frequency GNPs. The results show that rare alleles occurred randomly and frequently in the genome. A rare allele can only extend over a short genetic distance; therefore, any rare allelic pattern is unique, which imply different mechanisms of generation and evolution between rare GNPs and SNPs. Rare alleles evolve faster than other haplotypes and can persist 8 times longer in populations than single nucleotide mutations. The distributions of GNPs and SNPs were markedly different in terms of codon position and in synonymous and non-synonymous substitutions, which imply that GNP are mainly contribution to genetic divergence between species. An indel-associated model could well explain the characteristics of rare alleles, and their generation and maintenance, with comparison of gene evolution patterns in close related species, which provide a new evidence for genetic evolution theory. |
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