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.