Fig 1.
Molecular characterizations of the 41 genes in 21 chloroplast genomes of the genus Arachis.
(A) Distributions of overall GC, GC12, and GC3s contents. (B) The PR2 plot. (C) The neutrality plot. (D) The base ratios of overall 41 genes in 21 chloroplast genomes.
Fig 2.
Codon usage patterns in chloroplast genes of the genus Arachis.
(A) Effective number of codon (ENC) vs. GC3s plot. The blue curve denotes the expected theoretical ENC values with no evolutionary constraint, the dots under the blue line indicate bias in the genes, and the dots above the line denote little or no bias but homogeneous codon usage in these gene sequences. (B) The ENC values for individual genes. (C) Relationships between the ENC values (normalized to the range of the CBI distributions) and the CBI values of 41 genes in 21 chloroplast genomes of the genus Arachis.
Fig 3.
Correlation coefficients of the correlation analyses among the codon usage parameters of the 41 genes in 21 chloroplast genomes of genus Arachis.
“Ami No” represents the total number of amino acids based on the gene.
Fig 4.
The relative synonymous codon usage (RSCU) values of 41 genes in 21 chloroplast genomes of the genus Arachis.
The names of amino acids are abbreviated and listed along the Y-axis. “Stop” represents the terminal codons of UAA, UAG, and UGA. The CQ values represent the total codons in the 924 coding sequences.
Fig 5.
Heat map of the relative synonymous codon usage (RSCU) values for the 41 genes in 21 chloroplast genomes of the genus Arachis.
The blank boxes indicate the absence of corresponding codons for certain amino acids.
Fig 6.
Variations among 21 chloroplast genomes of the genus Arachis based on the Euclidean distances calculated by the RSCU values of 41 genes in each chloroplast genome and the correspondence analysis (presented in the inset graph) of 21 chloroplast genomes of the genus Arachis.
Table 1.
Base usage diversity of 41 genes in 21 chloroplast genomes of the genus Arachis.
Data are presented as mean ± standard deviation. Two copies of each of the three genes (i.e., rps12, rps7, and ycf2) are detected in each of the 21 chloroplast genomes.
Fig 7.
Degree of base usage divergences of 41 genes in 21 chloroplast genomes of the genus Arachis.
The X-axis represents the length of gene sequences.