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).