2.6 Whole-genome duplication (WGD) analysis

WGD analysis was performed using four genomes: V. vinifera(eudicots; Vvi), C. canephora (asterids; Cca), G. jasminoides (asterids; Gja), and S. tetraptera (asterids; Ste). Synteny analyses between and within species were surveyed using wgdi (Sun et al., 2021). Rectangles with different colors highlighted the collinear blocks containing at least 10 gene pairs. For each colinear gene pair, synonymous substitutions per synonymous site (Ksvalue) were calculated using the Nei-Gojobori (NG) approach implemented in PAML (Z. Yang, 2007) v4.9. The median Ks values for each collinear block were extracted to estimate the Ks distributions further using wgdi. The collinear blocks were classified into different groups according to their Ks values, then the genes produced were identified by the two most recent WGDs using wgdi (with ”-a” parameter).