Fig. 4: Evolutionary dynamics of the ancestral core-eudicot genes in extant Panax stipuleanatus genome.

a Co-expression network of the ancestral core-eudicot genes involved in the leaf development in extant P. stipuleanatus species. Eight gene clusters were defined according to their originations. Eu1–Eu7 are the seven ancestral core-eudicot chromosomes. Numbers below each ancestral chromosome (Eu1–Eu7) are the total identified ancestral genes. Gray dots in the middle are the ancestral genes that cannot be unassigned to the seven ancestral chromosomes. Gray lines indicate the ancestral gene interaction. Colors and numbers represented the functions and numbers of ancestral genes involved in the leaf development. b Ternary plot of expression patterns of ancestral genes in extant P. stipuleanatus genome. Each circle is a triad showing relative expression abundance in leaf, root and stem tissues for each ancestral gene. Triads in vertices correspond to the three tissue-dominant expression categories, whereas triads close to edges and between vertices correspond to three tissue-suppressed expression categories. Balanced triads are shown in gray. c Percentage of triads in each category of the ancestral genes (left) and boxplot of cytosine methylation for the ancestral genes (right). The 42 bars from top to bottom represent the duplicated ancestral core-eudicot chromosomes (Eu1–Eu7). Each ancestral chromosome contains six homologous genomic regions in extant P. stipuleanatus genome. Colors of the seven types of genes and names of each ancestral chromosome are the same as in Fig. 1. All ancestral genes identified in the 42 genomic regions were used to the statistical analyses. In right panel, the lower and upper whiskers of each colored box are the lowest (0.00) and highest (1.00) cytosine methylation level, respectively. The black solid lines within each box are media values. Lengths of the boxes are the interquartile range. d Expression dynamics of the protein-coding genes and non-coding RNAs of the 42 duplicated ancestral chromosomes in the leaf, root, and stem tissues. X- and Y-axis are expression diversity (Dj) and specificity (Sj) of the ancestral genes. Each symbol represents an ancestral chromosome. Differences in Dj and Sj values indicate high expression diversity among the ancestral chromosomes and expression specificity among the three tissues. The edges of each shade area are the error bands. Source data are provided as a Source Data file.