The pattern of codon usage in the chloroplast genome of Populus alba was investigated. Correspondence analysis （a commonly used multivariate statistical approach） and method of effective number of codons （ENc）-plo...The pattern of codon usage in the chloroplast genome of Populus alba was investigated. Correspondence analysis （a commonly used multivariate statistical approach） and method of effective number of codons （ENc）-plot were conducted to analyze synonymous codon usage. The results of correspondence analysis showed that the distribution of genes on the major axis was significantly correlated with the frequency of use of G＋C in synonymously variable third position of sense codon （GC3S）, （r=0.349）, and the positions of genes on the axis 2 and axis 3 were significantly correlated with CAI （r=-0.348, p〈0.01 and r=0.602, p〈0.01）. The ENc for most genes was similar to that for the expected ENc based on the GC3s, but several genes with low ENc values were lying below the expected curve. All of these data indicated that codon usage was dominated by a mutational bias in chloroplast gcnome ofP. alba. The selection in nature for translational efficiency only played a minor role in shaping codon usage in the chloroplast genome ofP alba.展开更多
DNA methylation is an important epigenetic regulation mechanism, which is catalyzed by DNA methyltransferases. In this study, eight DNA methyltransferase genes were identified in grape genome to analyze the selective ...DNA methylation is an important epigenetic regulation mechanism, which is catalyzed by DNA methyltransferases. In this study, eight DNA methyltransferase genes were identified in grape genome to analyze the selective pressure, gene expression and codon usage bias. The results showed grape DNA methyltransferase MET subfamily underwent relatively strong purifying selection during evolution, while chromomethylase CMT subfamily underwent positive selection during evolution. Under different abiotic(heat, drought or cold) stresses, the expression level of many grape DNA methyltransferase genes changed significantly. The expression level of these genes might be related with cis-regulatory elements of their promoters. The results of codon usage bias analysis showed that synonymous codon bias existed in grape DNA methyltransferase gene family, which might be affected by mutation pressure. These results laid a solid foundation for in-depth study of DNA methyltransferases in grape.展开更多
基金supported by the National High Tech Development Project of Chinathe 863 Program (Grant Nos.2007AA02Z329)the National Natural Science Foundation of China (Grant Nos.20060213024).
文摘The pattern of codon usage in the chloroplast genome of Populus alba was investigated. Correspondence analysis （a commonly used multivariate statistical approach） and method of effective number of codons （ENc）-plot were conducted to analyze synonymous codon usage. The results of correspondence analysis showed that the distribution of genes on the major axis was significantly correlated with the frequency of use of G＋C in synonymously variable third position of sense codon （GC3S）, （r=0.349）, and the positions of genes on the axis 2 and axis 3 were significantly correlated with CAI （r=-0.348, p〈0.01 and r=0.602, p〈0.01）. The ENc for most genes was similar to that for the expected ENc based on the GC3s, but several genes with low ENc values were lying below the expected curve. All of these data indicated that codon usage was dominated by a mutational bias in chloroplast gcnome ofP. alba. The selection in nature for translational efficiency only played a minor role in shaping codon usage in the chloroplast genome ofP alba.
基金Supported by Major Agricultural Application Technology Innovation Project of Shandong Province"Research and Application of Precision Control of Maturation and Product Innovation of Featured Brewing Grape"Major Agricultural Application Technology Innovation Project of Shandong Province"Development of Landmark Wines and Integrated Application of Key Technologies in Shandong Province"Agricultural Scientific and Technological Innovation Project of Shandong Academy of Agricultural Sciences(CXGC2016D01)
文摘DNA methylation is an important epigenetic regulation mechanism, which is catalyzed by DNA methyltransferases. In this study, eight DNA methyltransferase genes were identified in grape genome to analyze the selective pressure, gene expression and codon usage bias. The results showed grape DNA methyltransferase MET subfamily underwent relatively strong purifying selection during evolution, while chromomethylase CMT subfamily underwent positive selection during evolution. Under different abiotic(heat, drought or cold) stresses, the expression level of many grape DNA methyltransferase genes changed significantly. The expression level of these genes might be related with cis-regulatory elements of their promoters. The results of codon usage bias analysis showed that synonymous codon bias existed in grape DNA methyltransferase gene family, which might be affected by mutation pressure. These results laid a solid foundation for in-depth study of DNA methyltransferases in grape.
