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.