Comprehensive analysis of codon bias in 13 Ganoderma mitochondrial genomes

Abstract

Introduction: Codon 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.

Methods: In this study, we investigated the codon bias of 12 mitochondrial core protein-coding genes (PCGs) in 9 Ganoderma species, including 13 Ganoderma strains.

Results: The 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.

Discussion: This study deepens our insight into the synonymous codon usage characteristics, genetics, and evolution of this important fungal group.

Keywords: codon usage; fungi; genetics; mitochondrial genome; natural selection.

Figure 1

The codon usage indicators of twelve core protein-coding genes in 13 Ganoderma strains. (A) ENc, GC1, GC2, GC3, GC3s indicators. (B) CAI, CBI, FOP, Gravy, Aromo indicators.

Figure 2

Pearson’s correlation analysis heatmap of codon usage indicators of 13 Ganoderma strains. The color of the blocks in the heatmap changes from yellow to blue, indicating an increase in the correlation coefficient. A single asterisk signifies a statistically significant correlation between the two (Continued)FIGURE 2 (Continued)indicators at the p < 0.05 level, while two asterisks symbolize a significant correlation between the two indicators at the p < 0.01 level. The 13 Ganoderma species are G. applanatum, G. leucocontextum, G. tsugae, G. sinense, G. subamboinense s118, G. calidophilum, G. meredithae, G. lucidum KC763799, G. lucidum s26, G. lucidum s37, G. lingzhi s62, G. lingzhi s74, and G. lingzhi s8, from left to right and from top to bottom.

Figure 3

Neutrality plot analysis of GC12 and the third codon position (GC3) for the entire coding DNA sequence of 13 Ganoderma strains. (A) G. applanatum; (B) G. leucocontextum; (C) G. tsugae; (D) G. sinense; (E) G. subamboinense s118; (F) G. calidophilum; (G) G. meredithae; (H) G. lucidum KC763799; (I) G. lucidum s26; (J) G. lucidum s37; (K) G. lingzhi s62; (L) G. lingzhi s74; (M) G. lingzhi s8.

Figure 4

ENC-GC3 plot analysis of 12 core PCGs in 13 Ganoderma strains. The solid line represents the expected curve when codon usage bias is affected only by mutation pressure. (A) G. applanatum; (B) G. leucocontextum; (C) G. tsugae; (D) G. sinense; (E) G. subamboinense s118; (F) G. calidophilum; (G) G. meredithae; (H) G. lucidum KC763799; (I) G. lucidum s26; (J) G. lucidum s37; (K) G. lingzhi s62; (L) G. lingzhi s74; (M) G. lingzhi s8.

Figure 5

Parity Rule 2 (PR2) plot analysis of 12 core PCGs in 13 Ganoderma strains. (A) G. applanatum; (B) G. leucocontextum; (C) G. tsugae; (D) G. sinense; (E) G. subamboinense s118; (F) G. calidophilum; (G) G. meredithae; (H) G. lucidum KC763799; (I) G. lucidum s26; (J) G. lucidum s37; (K) G. lingzhi s62; (L) G. lingzhi s74; (M) G. lingzhi s8.

Figure 6

Correspondence analysis (COA) based on the relative synonymous codon usage (RSCU) values of 12 mitochondrial genes from 13 Ganoderma strains. Purple represents the cox gene, red represents the nad gene, green represents the atp6 gene, blue represents the cob gene, and yellow represents the rps3 gene. (A) G. applanatum; (B) G. leucocontextum; (C) G. tsugae; (D) G. sinense; (E) G. subamboinense s118; (F) G. calidophilum; (G) G. meredithae; (H) G. lucidum KC763799; (I) G. lucidum s26; (J) G. lucidum s37; (K) G. lingzhi s62; (L) G. lingzhi s74; (M) G. lingzhi s8.

Figure 7

Relative synonymous codon usage (RSCU) analysis of 12 mitochondrial genes from 13 Ganoderma strains. (A) G. applanatum; (B) G. leucocontextum; (C) G. tsugae; (D) G. sinense; (E) G. subamboinense s118; (F) G. calidophilum; (G) G. meredithae; (H) G. lucidum KC763799; (I) G. lucidum s26; (J) G. lucidum s37; (K) G. lingzhi s62; (L) G. lingzhi s74; (M) G. lingzhi s8.

Figure 8

Optimal codon analysis of 13 Ganoderma strains (ΔRSCU>0.08 and RSCU>1) are marked in purple. Highly expressed codons (ΔRSCU>0.08) are marked in yellow, and high-frequency codons (RSCU>1) are marked in blue.

Figure 9

Relationship inference of 13 Ganoderma strains based on the Bayesian inference (BI) (A) method and relative synonymous codon usage (RSCU)-based hierarchical clustering (B).