Figure Legends

Figure 1. Overview of the morphology and genome assembly ofSinoswertia tetraptera. (a) Morphology of the chasmogamous (CH) and cleistogamous (CL) flowers and petals. Scale bars, 1 cm. (b) Genome assembly and annotations. From inside to outside: (I) gene density in 500kb sliding windows, (II) GC density in 500kb sliding windows, (III) Gypsy density in 500kb sliding windows, (IV) Copia density in 500kb sliding windows, (V) density of long terminal repeats (LTR) in 500kb sliding windows, (VI) density of TE in 500kb sliding windows. (VIII) the density of SNP in 50kb sliding windows.
Figure 2. Genome evolution. (a) Chronogram showing divergence times and genome duplications in angiosperms (Gentianales, Asterids, Rosid, Eudicot, and Monocot), with node age and 95% confidence intervals. The lengths of light blue labels represent the random values in Ma. Dots with * represent resolved polyploidization events in previous studies; others indicate new events we identified in this study, while D indicates duplication events and T triplication events. Pie charts show the proportions of gene families among the 12 species that underwent expansion or contraction. (b) Functional enrichment analysis of genes belonging to the last WGD which different expressed between dimorphic flowers (hear called most recent WGD DEGs) and expanded in S. tetraptera . The length of bars represents the number of genes. The enriched GO terms of biological progress with corrected P -value <0.01 are presented. Terms presented after clusterProfiler simplify. (c) After evolutionary rate correction among the various species, the distribution of average synonymous substitution levels (Ks ) between syntenic blocks was raised by different color lines for each species. (I) Ks distribution showing Ks distribution from paralogs within a species. (II)Ks distribution showing Ks from orthologs between S. tetraptera and each of four species indicated by dashed lines. (d) Synthetic blocks (involving ≥ 10 colinear genes) between genomes involving S. tetraptera and V. vinifera. The corresponding median Ks value is shown for each block, and the various colored rectangles represent polyploidization events. The homologous chromosomes in grape were selected and are presented in blue.
Figure 3. MADS-box genes and genetic regulation of closed and open dimorphic flowers of S. tetraptera . (a) A phylogenetic tree of the MADS-box gene family. The numbers of the AGL15/18 sub-class members within five species and their significance were obtained by the LSD test after Bonferroni (BH) correction. (b) The level of plant hormones participating in bloom regulation in CH and CL flowers. **p < 0.01, Student’s t-test. (c) A proposed pathway for the control of closed or open dimorphic flowers. Gene expression profiles are presented in the heatmap alongside the gene names. The bar shows the expression level of each gene. Low to high expression is indicated by light yellow to red.
Figure 4. Differentiation between CH and CL flowers. (a) The floral size and the level of cytokinin differ between CH and CL flowers. **p < 0.01, Student’s t-test. The lower part of the figure presents a probable cytokinin-dependent pathway controlling the contrasting sizes of dimorphic flowers. Gene expression profiles are presented in the heatmap alongside the gene names. (b) Gene expression profiles involved in flower pigment biosynthesis of CH and CL flowers. (c) Gene expression profiles of the SWEET gene family members, comparing CH and CL flowers.
Figure 5. Iridoid biosynthesis in S. tetraptera. (a) Concentration of four iridoids in seven tissues. Different letters within each part indicate significance according to the LSD test after Bonferroni (BH) correction. (b) Sub-network for the leaf and flower module of iridoid biosynthesis. (c) The probable biosynthesis pathway of four iridoids. Gene expression profiles are presented in the heatmap alongside the gene names.