List of Figures
Figure 1 Morphological features and genome evolution of C.
rotundifolia . (a) The succulent leaf, leaf abaxial surface, flower
(without petals), and fruit of C. rotundifolia (top).
Correspondingly, the vegetative and reproductive organs of grape (down).
(b) Divergency history between Cissus and grape within the
phylogeny of flowering plants. Age estimates of each node are based on
342 single copy genes from 13 representative plant species. The WGD or
WGT were indicated on the corresponding branches. The number of gene
family expansion and contraction was indicated along the related
branches. (c) Distribution of genomic features of Cissus genome.
Each track shows the GC content, repetitive sequences distribution, gene
density, and gene expression profile in different tissues from outside
to inside. (d) Estimation of LTR activity shows a very recent burst
event in Cissus in less than 90.77 kya and a much more severe
invasion of LTR than grape. (e) Distribution of Ks for the whole
paranome of Cissus and cross-comparison between Cissus and
grape. Right corner of the image showed the segmental duplications
within the chromosomes.
Figure 2 Gross chromosomal rearrangement underlying C.
rotundifolia modern 12 chromosomes. (a) Macro-synteny patterns betweenC. rotundifolia and V. vinifera , the C.
rotundifolia chromosomes were numbered according to their physical
length from long to short. (b) Seven colored codes were used according
to the earlier prediction of ancient seven chromosomes of AEK pre-γ, the
schematic representation of paralogous regions derived from a
grape–cacao–peach comparison (Freeling, 2009). The karyotypes ofC. rotundifolia and V. vinifera were derived from syntenic
comparison with AEK pre-γ and were defined by the occurrence of the
syntenic regions as linked clusters in AEK pre-γ, independently of
intrachromosomal rearrangements. The evolutionary events were predicted
according to the more parsimonious model of evolution. (c) The syntenic
relationship among Cissus , grape, and Amborella . EachA. trichopoda scaffold region aligns with up to three regions in
either Cissus or grape, which were highlighted in red. Shades
represent matching gene pairs. (d) Statistic of syntenic regions amongA. trichopoda , V. vinifera and C. rotundifolia . The
subset of the proportion of genes in syntenic blocks to the whole genome
was indicated on the histograms.
Figure 3 Evolution history of functional profiles of C.
rotundifolia genome. (a) Heatmap shows categorized orthogroups that
have significantly increased paralogous numbers in Cissuscompared with other angiosperms analyzed. (b) The satter plot displayed
the expanded orthogroups in five succulent plants and 13 other
non-succulent plants. Numbers in square brackets associated with circle
sizes stand for -log (P -adjust), where P -adjust is thep -value of the binomial test adjusted for multiple testing. 1–18
are terpene synthase, plant self-incompatibility protein S1, hsp20/alpha
crystallin family protein, aspartic proteinase nepenthesin-1 precursor,
eukaryotic aspartyl protease family protein, leucine rich repeat
protein, F-box domain and LRR containing protein, MATE efflux family
protein, nuclear transcription factor Y subunit,
UDP-glycosyltransferase, serine/threonine-protein kinase receptor
precursor, retrotransposon protein, disease resistance RPP13-like
protein 1, cysteine-rich receptor-like protein kinase, leucine-rich
repeat receptor-like protein kinase family protein, retrotransposon
protein, wall-associated receptor kinase, and F-box family protein. (c)
GO categories with an overrepresented number of tandemly duplicated
genes in expanded orthogroups encompassing different evolutionary
periods of Cissus (upper) and the functional bias of tandem
duplicate genes retention in grape (lower). The number of TD events was
indicated on the branches. (d) Percentage of GO categories from expanded
lineage-specific TD in succulent plants and other non-succulent plants.
Cellular component and resistance categories in two subgroups were
tested by a two-sample t-test.
Figure 4 The CAM pathway in C. rotundifolia . (a) The diurnal
variation of titratable acidity in C. rotundifolialeaves. (b) Expression patterns and cis -regulatory
elements of CAM-related genes across the diurnal variation. The
expression level of each gene was shown in the log10-transformed method.
The numbers of five circadian clock-related motifs, including G-box
element, evening element (EE), morning element (MOM), CIRCADIAN CLOCK
ASSOCIATED 1 (ACC1) binding site, and TCP15 were shown in the 2-kb
promoter region of each gene. (c) The overview of the CAM pathway. The
carboxylation process (dark period) was shown in the left part, and the
decarboxylation process (light period) was shown in the right part. The
enzymes were marked in blue and green, respectively, with corresponding
expression profiles. A network was constructed for Cluster 4 (d) and
Cluster5 (e) using ARACNE. The top 1 % of each network was highlighted
by yellow circle, and blue nodes with greater than 10 edges were CAM
related genes in C. rotundifolia . The yellow and blue
nodes were annotated in Table S29.