Comparative analysis of codon usage between Gossypium hirsutum and G. barbadense mitochondrial genomes

Abstract

Gossypium hirsutum and G. barbadense mitochondrial genomes were analyzed to understand the factors shaping codon usage. While most analyses of codon usage suggest minimal to no bias, nucleotide composition, specifically GC content, was significantly correlated with codon usage. In general, both mitochondrial genomes favor codons that end in A or U, with a secondary preference for pyrimidine rich codons. These observations are similar to previous reports of codon usage in cotton nuclear genomes, possibly suggestive of a general bias spanning genomic compartment. Although evidence for codon usage bias is weak for most genes, we identified six genes (i.e. atp8, atp9, sdh3, sdh4, mttB and rpl2) with significant nonrandom codon usage. In general, we find multiple factors that influence cotton mitochondrial genome codon usage, which may include selection in a subset of genes.

The Mitogenome of Sedum plumbizincicola (Crassulaceae): Insights into RNA Editing, Lateral Gene Transfer, and Phylogenetic Implications

“…These results were listed in Table S5 . Generally, ENC values ≤ 35 indicate high codon preference [ 56 , 59 , 60 ]. In the present analyses, the ENC values of all 31 PCGs both before (39.09–61) and after RNA editing (38.15–61) were higher than 35, which indicates mitochondrial genes of S. plumbizincicola lacked strong codon bias.…”

“…In particular, the neutrality plot analysis could be used to quantify the extent of mutation against natural selection [ 61 , 62 ]. However, this analysis approach was only performed in a few plant mitogenomes at the genomic level [ 56 , 114 ]. Taking S. plumbizincicola as an example, our study executed neutrality plot analyses at both genomic and transcriptomic levels.…”

“…The GC12 and GC3 were calculated by using MEGA X 10.0.5 [ 55 ]. In addition, the ENC-GC3s plot analysis has proven to be a highly efficient tool for verifying the main driving factor of mutation pressure or natural selection [ 56 , 57 , 58 , 59 , 60 ]. Meanwhile, the neutrality plot (GC12 vs. GC3) can be used to estimate the extent of directional mutation pressure against natural selection in the codons.…”

Genome-wide analysis of codon usage in sesame (Sesamum indicum L.)

“…translational selection [28][29][30][31], gene expression level [32][33][34][35][36][37][38][39], gene length [40][41][42][43], function of the gene [44], the frequency rate of recombination [28,45], secondary structure of the protein [46,47,48], protein amino acid composition [49,50,51], the evolutionary age of the genes [52], the length of the intron [53], tRNA abundance [5,54,55,56], and environmental stress [57]. Codon usage indices are used to help the tabulation and investigation of codon usage and they can reduce the codon usage data into a useful summary [7,10,28,33,37,53,67,70,74].…”

“…Mutation is responsible to generate codon diversity while reduction of codon diversity is achieved mainly through natural selection. Further factors suggested to affect CUB include compositional constraints of genes [ 23 , 24 , 25 , 26 ], translational selection [ 27 , 28 , 29 , 30 ], gene expression level [ 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 ], gene length [ 39 , 40 , 41 , 42 ], function of the gene [ 43 ], the frequency rate of recombination [ 27 , 44 ], secondary structure of the protein [ 45 , 46 , 47 ], protein amino acid composition [ 48 , 49 , 50 ], the evolutionary age of the genes [ 51 ], the length of the intron [ 52 ], tRNA abundance [ 5 , 53 , 54 , 55 ], and environmental stress [ 56 ]. Codon usage indices are used to help the tabulation and investigation of codon usage and they can reduce the codon usage data into a useful summary [ 7 , 9 , 27 , 32 , 36 , 52 , 57 , 58 , 59 ].…”