Codon usage bias and evolution analysis in the mitochondrial genome of Mesona chinensis Benth

Mesona chinensis Benth (MCB) is an edible and medicinal plant in southern China and Southeast Asian countries. Mitochondria, semi-autonomous organelles in eukaryotic cells, contain their own genome (mitogenome) and are involved in various cellular processes. Codons are the core elements of protein translation in gene-coding regions. It is of great significance to analyze the characteristics of codon usage in gene-coding regions for gene function and phylogenetic studies. Here, the codon usage pattern and the factors affecting codon usage bias (CUB), and the cluster and phylogenetic analysis based on mitogenomes were determined. Results of nucleotide composition analysis showed an unequal distribution of T, G, A, and C nucleotides and AT bias in MCB mitogenome. The GC, GC1, GC2, GC3 content, codon adaption index (CAI), and effective number codon (ENC) of MCB mitogenome were 43.09%, 48.37%, 42.67%, 38.22%, 0.632, and 55.539, respectively, while those of each gene ranged from 35.61% to 51.85%, 36.25% to 56.69%, 33.46% to 47.76%, 23.08% to 58.15%, 37.81 to 60.02, and 0.564 to 0.680, respectively. 18 out of 28 genes showed the highest GC1 content and the lowest GC3 content, and the general order of GC content in different codon positions was GC1 > GC2 > GC3. Further analysis of the neutrality plot, ENC-plot, and PR2-bias plot revealed that the CUB of MCB mitogenome was affected by natural selection and mutation. Seven optimal codons, TTG, GAC, TCA, AGA, ACC, GGG, and ATA were determined in MCB mitogenome. The phylogenetic tree based on mitogenome sequences and the cluster analysis based on relative synonymous codon usage (RSCU) values indicated that the CUB of mitogenome might have to do with the genetic relationship among species. Overall, the current study positively contributed to the molecular mechanism of biological adaptation and the evolutionary relationship of MCB.