Figure 2. Heatmaps showing correlation between codon usage and GC3 for chloroplast genes among two Pisum species.
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Abstract: This study was attempted to focus on the pattern of codon usage bias (CUB) of chloroplast genes in two species of Pisum viz. P. fulvum and P. sativum and to identify the factors which influence CUB. Bioinformatic tools were used to understand codon usage pattern in the protein-coding sequences of Pisum chloroplast genomes. It was found that GC content was lower than AT content in the genes. Low synonymous codon usage order (SCUO) values of genes indicated low CUB in chloroplast genes of Pisum species. Heatmaps showed positive correlations of GC3 with all the GC and AT ending codons. Neutrality plot analysis revealed that natural selection might have played a prominent role over mutation pressure in sculpturing the CUB of chloroplast genes in these two taxa. Positive correlation between SCUO and mRNA free energy (mFE) suggested that higher energy release by entire mRNA was related to high degree of CUB. Further, highly significant (p < .01) negative correlation was found between parameters in pair i.e. mFE-GC, mFE-GC1, mFE-GC2 and mFE for entire mRNA-GC3. This pointed out that higher GC content might have influenced lesser energy release by mRNA molecules of chloroplast genes.
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Genetics Biology Medicine Related Papers Abstract: Codon usage bias (CUB) is a unique property of genome which refers to non-random usage of synonymous codons in coding sequences. The present study makes an attempt to find out the pattern of CUB in chloroplast (cp) genes among three tea species, i.e., Camellia sinensis var. assamica (Assam tea), Camellia sinensis var. sinensis (Chinese tea) and Camellia pubicosta (wild tea species) as no work on CUB was reported earlier. To understand the patterns of codon usage among the cp genes of three tea groups, we used bioinformatic tools to investigate the protein coding sequences of cp genes. In our present study, the mean nucleobase T was the highest whereas C was the lowest in all the three tea groups. The overall AT content was more than GC content, i.e., genes were AT rich. The scaled chi-square (SCS) value indicated that the CUB of cp genes was low. The codon CGT (Arg) was over-represented in C. sinensis var. sinensis whereas GGA (Pro) was over-represented in C. pubicosta species. Heatmap study revealed that most of the GC ending codons showed positive correlations between codon usage and GC3 while AT ending codons exhibited negative correlations. From neutrality plot analysis, it was evident that natural selection had played a major role, while mutation pressure exerted a minor effect in the CUB of cp genes in three tea groups. Highly significant (P<0.01) positive correlation was found between SCS and synonymous codon usage order (SCUO) of cp genes which suggested that high expression of cp genes was associated with high degree of CUB.
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Abstract: Miscanthus is not only a perennial fiber biomass crop, but also valuable breeding resource for its low-nutrient requirements, photosynthetic efficiency and strong adaptability to environment. In the present study, the codon usage patterns of five different Miscanthus plants and other two related species were systematically analyzed. The results indicated that the cp genomes of the seven representative species were preference to A/T bases and A/T-ending codons. In addition, 21 common high-frequency codons and 4-11 optimal codons were detected in the seven chloroplast genomes. The results of ENc-plot, PR2-plot and neutrality analysis revealed the codon usage patterns of the seven chloroplast genomes are influenced by multiple factors, in which nature selection is the main influencing factor. Comparative analysis of the codon usage frequencies between the seven representative species and four model organisms suggested that Arabidopsis thaliana, Populus trichocarpa and Saccharomyces cerevisiae could be considered as preferential appropriate exogenous expression receptors. These results might not only provide important reference information for evolutionary analysis, but also shed light on the way to improve the expression efficiency of exogenous gene in transgenic research based on codon optimization.
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Abstract: Miscanthus is not only a perennial fiber biomass crop, but also valuable breeding resource for its low-nutrient requirements, photosynthetic efficiency and strong adaptability to environment. In the present study, the codon usage patterns of five different Miscanthus plants and other two related species were systematically analyzed. The results indicated that the cp genomes of the seven representative species were preference to A/T bases and A/T-ending codons. In addition, 21 common high-frequency codons and 4-11 optimal codons were detected in the seven chloroplast genomes. The results of ENc-plot, PR2-plot and neutrality analysis revealed the codon usage patterns of the seven chloroplast genomes are influenced by multiple factors, in which nature selection is the main influencing factor. Comparative analysis of the codon usage frequencies between the seven representative species and four model organisms suggested that Arabidopsis thaliana, Populus trichocarpa and Saccharomyces cerevisiae could be considered as preferential appropriate exogenous expression receptors. These results might not only provide important reference information for evolutionary analysis, but also shed light on the way to improve the expression efficiency of exogenous gene in transgenic research based on codon optimization.
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