Analysis Of Evolutionary Rate In Protein Coding Gene Of Human Genome

With the completion of more and more mammalian genome sequence, study of human genome evolution has become possible. Gene evolution is the foundation of biological evolution. By comparing the human and other mammalian genome sequence, analysis of the nucleotide substitution patterns could further explore the causes of biological evolution. We aligned the primates (human and chimpanzee) and mammalian (mouse and dog) genome sequences, then their homologous genes were seriously analyzed, To explore the trends in the evolution of human chromosomes, the dynamics underlying the evolution of human chromosomes was also further studied. Furthermore, the correlation between evolution rates and transposable elements of human tissue-specific genes (a special class of human genes) was analyzed. The results showed that 1) Both human and chimpanzee chromosomes featured significantly different synonymous substitution rates (dS) values, indicating that accumulation of synonymous substitutions on human and chimpanzee chromosomes have been nonparallel. And the dS and non-synonymous substitution rates (dN) is homogeneous across different phylogeny branches, suggesting that the relevant genes have subjected to similar selection for base substitution rates. 2) Local chromatin environment (such as GC content and gene density) and recombination rates may contribute to accumulation of both types of substitutions on human chromosomes. In addition, microRNAs located within introns of protein coding genes also affected the evolution of their host genes. 3) Different category of human tissue-specific genes featured divergent values of dN/dS, suggesting that they may have been subjected to divergent evolutionary forces. 4) Transposable elements probably had very significant contribution to the functional divergence of human tissue-specific genes. TEs densities in both exonic and intronic regions showed a strong correlation with dN/dS values, revealing that the evolution of exons had been coordinated with that of flanking introns. Our findings may provide important clues for delineating the evolution and divergence of primate chromosomes.