Supplementary Fig.1 The distribution of synonymous codons along the first and second axes of the correspondence analysis - The dot represents C/G ending codons and x represents A/U ending codons. a. T. aestivum, b. H. vulgare, c. B. distachyon

a. T. aestivum b. H. vulgare

c. B. distachyon

Supplementary Fig.2 Genomic location of orthologous segments – Genomic location of orthologous segments identified among chloroplast genome sequences of T. aestivum, H. vulgare,and B. distachyon are visualized using the GMV program. (A) Dot-plot visualization. (B) Chrom-link visualization.

(A) Dot-plot visualization (B) Chrom-link visualization

Supplementary Fig.3 Synonymous codon usage (SCUO) and GC composition - Visualization of the correlation between synonymous codon usage bias and GC measured by synonymous codon usage orderliness (SCUO) and GC composition of the three chloroplast genomes.

a. T. aestivum b. H. vulgare

c. B. distachyon