Transcript free energy positively correlates with codon usage bias in mitochondrial genes of Calypogeia species (Calypogeiaceae, Marchantiophyta)

Abstract

The present study attempts to focus on the pattern of codon usage bias (CUB) in mitochondrial genes among four species of Calypogeia viz. C. arguta, C. integristipula, C. neogaea and C. suecica along with the factors influencing their CUB as no work was reported yet. The four taxa exhibit noticeable difference in their morphological features, habitat preference and growth forms. To understand the patterns of codon usage in Calypogeia mitochondrial genomes, we used bioinformatic tools to analyze the mitochondrial protein-coding sequences of four Calypogeia. In our current study, the mean nucleobase T was the highest while G was the lowest in all four species. The overall GC content was higher than AT content i.e. genes were AT rich. The CUB was low in mitochondrial genes of C. arguta, C. integristipula, C. neogaea and C. suecica, respectively as revealed from low synonymous codon usage order (SCUO) values. Heat map study revealed that most of the GC and AT ending codons showed positive correlations between codon usage and GC3. From the neutrality plot, the slope of the regression line indicated that natural selection might have played a major role over mutation pressure in shaping the CUB of mitochondrial genes in these four taxa. Highly significant (p < .01) correlation was found between mRNA free energy (mFE) and SCUO for entire mRNA which suggested that the release of higher energy by entire mRNA is associated with higher degree of codon usage bias. Further, highly significant (p < .01) negative correlation of mFE for entire mRNA was found with GC, GC1, GC2 and GC3 in all the four taxa. This indicated that higher GC content might have induced the release of lesser energy by mRNA molecules.