Comprehensive analysis of codon bias in 13 Ganoderma mitochondrial genomes

Abstract

IntroductionCodon usage bias is a prevalent phenomenon observed across various species and genes. However, the specific attributes of codon usage in the mitochondrial genome of Ganoderma species remain unknown.MethodsIn this study, we investigated the codon bias of 12 mitochondrial core protein-coding genes (PCGs) in 9 Ganoderma species, including 13 Ganoderma strains.ResultsThe codons of all Ganoderma strains showed a preference for ending in A/T. Additionally, correlations between codon base composition and the codon adaptation index (CAI), codon bias index (CBI) and frequency of optimal codons (FOP) were identified, demonstrating the impact of base composition on codon bias. Various base bias indicators were found to vary between or within Ganoderma strains, including GC3s, the CAI, the CBI, and the FOP. The results also revealed that the mitochondrial core PCGs of Ganoderma have an average effective number of codons (ENC) lower than 35, indicating strong bias toward certain codons. Evidence from neutrality plot and PR2-bias plot analysis indicates that natural selection is a major factor affecting codon bias in Ganoderma. Additionally, 11 to 22 optimal codons (ΔRSCU>0.08 and RSCU>1) were identified in 13 Ganoderma strains, with GCA, AUC, and UUC being the most widely used optimal codons in Ganoderma. By analyzing the combined mitochondrial sequences and relative synonymous codon usage (RSCU) values, the genetic relationships between or within Ganoderma strains were determined, indicating variations between them. Nevertheless, RSCU-based analysis illustrated the intra- and interspecies relationships of certain Ganoderma species.DiscussionThis study deepens our insight into the synonymous codon usage characteristics, genetics, and evolution of this important fungal group.

Multichromosomal Mitochondrial Genome of Punica granatum: Comparative Evolutionary Analysis and Gene Transformation from chloroplast genomes

“…The result was similar to the study in Salvia o cinalis [53], Leucaena trichandra [54] and Pereskia aculeata [55]. The nad4 gene possessed 39 potential RNA editing sites and was the most edited of pomegranate mitogenome, which was supported by other studies [14,39].…”

“…Codon usage preference is usually considered to be the result of the tendency to develop relative equilibrium within cells during species evolution, and codons with a RSCU greater than 1 are considered to be used by amino acid preference [17,[37][38][39]. The result indicated that Phe, Ile and Glu were the most common amino acids, and Met and Ter were much less common in the P. granatum mitogenome.…”

Multichromosomal mitochondrial genome of Punica granatum: comparative evolutionary analysis and gene transformation from chloroplast genomes

“…The result was similar to the study in Salvia officinalis [ 55 ], Leucaena trichandra [ 56 ] and Pereskia aculeata [ 57 ]. The nad4 gene possessed 39 potential RNA editing sites and was the most edited of pomegranate mitogenome, which was supported by other studies [ 14 , 41 ].…”

“…Codon usage preference is usually considered to be the result of the tendency to develop relative equilibrium within cells during species evolution, and codons with a RSCU greater than 1 are considered to be used by amino acid preference [ 17 , 39 – 41 ]. The result indicated that Phe, Ile and Glu were the most common amino acids, and Met and Ter were much less common in the P. granatum mitogenome.…”

Bioinformatic Analysis of Codon Usage Bias of HSP20 Genes in Four Cruciferous Species

“…At present, CUB analyses based on plant genomes are highly available due to the extensive sequencing of nuclei and organellar genomes, leading to valid and credible results [ 4 , 15 ]. Accumulating advances based on the genomes revealed that several factors, in particular natural selection, played a significant role in CUB [ 10 , 16 , 17 ]. Conversely, the significance of CUB in gene families has not been well studied.…”