Analysis Of Mitochondrial Genome Codon Preference And Evolutionary Relationships In The Family

Coding codes of same amino acids are defined as the synonymous codons. In the biological system, even among the same species between different genetic populations, their synonymous codon usage frequency exhibit differences, it is called synonymous codon usage bias. Codon usage bias is considered to be the result of long-term evolution. Due to the course of evolution, usage bias was affected by multiple factors such as the external environment and internal interaction. Thus, plotting the codon bias and the internal factors lead to this certain formation of the preference will provide important implications in understanding the characterization of a species' genome, and will shed light in the molecular evolution and ecological adaptation studies.Compared to nuclear genes, mitochondrial DNA is quite unique in copy mode, molecular size, genetic pattern, rate of evolution and other characteristics In the part of the mitochondrial coding genes, the phenomenon of using unbalanced codon is widespread. In fact, since the molecular size of the mitochondrial genome is small and inherited independently, thus they will have some integrity and specificity advantages in analyses of codon usage preferences.Hynobiidae belongs to the Amphibia:Caudata, as one of the main groups, possess great significance and value in urodeles evolutionary studies. At present, many complete mitochondrial genome sequencing of the Asiatic salamander species has been completed, but the codon preferences have not been studied. Therefore, this research used the relevant analysis, principal component analysis and bioinformatics analysis of neutral plot, in aim to discuss 20 kinds of Asiatic salamander animal mitochondrial genome codon usage patterns; revealing the Asiatic salamander species during evolution, mutation and neutral direction to choose which one is to determine mitochondrial genome codon preferences model is the dominant factor. In addition, based on codon usage bias phylogenetic relationships and build other molecular methods for phylogenetic tree contrast, expectations for research Hynobiidae genetic evolution and provide a new way of thinking. The results are as follows:1. In 20 kind of Asiatic salamander mitochondrial protein-coding gene sequences, the GC content are below 40%, synonymous codon third GC content (GC3s) is less than 30%, all less than 50%, show the AT base bias. Because of the difference between the base composition, NNT and the NNA type codon has a codon usage bias. In addition,20 Hynobiidae animals' mitochondrial protein-coding genes have preference in codon usage, and similar patterns were observed in each species, its preference differences varied exhibits preference at the same time not, that Hynobiidae mitochondrial genome has conserved a certain degree during evolution.2. ENC and GC3s plotting analysis showed that most of the points genes are located outside or below the standard curve, low fit, as well as other factors described mutation pressure to participate in the Hynobiidae mitochondrial protein-coding gene codon preferences formation. At the same time, based on the value RSCU principal component analysis, the first principal component can only explain part of the amount of codon usage preferences change. After applying the correlation analysis of the heavy weight of each factor analysis, the results show the main factors preference mitochondrial protein-coding gene codon performance of different species travel in the opposite sex in Hynobiidae. By drawing neutral, ENC drawing, as well as the results of PCA COA's unified analysis. The results show preference, the pressure of natural selection and mutation interaction Hynobiidae influence mitochondrial protein-coding gene codon, but natural selection is leading factor. Impact of each single factor, which exhibits effects among different species together in a joint action of the way in which the probability of optimal codons (Fop), hydrophobic (Gravy) and aromatic (Amoro), respectively, as factors closely related to codon bias; and gene length (L_aa) and expression level as factors of codon bias are also affected.3. Research on Hynobiidae mitochondrial genome codon usage and tRNA anti-codon correspondence between a statistical analysis. The results show that the CCP identified Hynobiidae synonymous codon family group of 22, including 12 sets of synonymous codons and tRNA optimal presence strict anti-codons match the codon mixed group contains three groups, and the remaining seven groups are not included in fully with the tRNA molecule anticodon match type, but by the third codon point swing and binding. Taken together, these results speculate, tRNA abundance Hynobiidae mitochondrial genome codon bias on the smaller, more indirect effects exhibited characteristics of the specific mechanism needs further analysis.4. Generally, it is believed that the closer the genetic relationship of species codon usage pattern should be more similar. Therefore, this study based on mitochondrial protein-coding gene 13 codon usage (RSCU value) as an index cluster analysis, the phylogenetic relationships of the species as a reference. After the clustering results and has been proven accurate molecular data have taxonomic significance of comparing research by constructing the mitochondrial protein coding sequence datasets using BI and ML phylogenetic tree was constructed. The results show that both the comparison and phylogenetic clustering results inconsistent results, relationships among the species and mitochondrial protein-coding genes CDS difference in size have a certain relationship. Closer to the codon bias based clustering results, although not as phylogenetic relationship based on CDS's phylogenetic relationships, but some studies have shown that phylogenetic classification is not perfect means of settlement. Further research will measure the codon bias index binding, clustering together, using a new digital-analog means, it would be desirable to improve the resolution and reliability of clustering results for the traditional morphological taxonomy and the molecular phylogenetic analysis provides supplementary and reference.