Article Figures & Data
Figures
- Figure 1.
Comparative analysis of the covariance structures of metabolites, transcripts, and profiles in tomato and pepper fruits. Similarity analysis is shown for the covariance structures of metabolites (A), transcripts (B), and integrated profiles (C; metabolite and transcript) over eight and 10 development and ripening stages from tomato and pepper, respectively. A similarity score was calculated for every pair of periods, each spanning four stages in development and ripening, based on the corresponding PCs (see “Materials and Methods”). The similarity score ranges from 0 to 1, with 0 indicating equality of the compared covariance structures. The results are displayed in the form of a heat map, with the color key included at the bottom.
- Figure 2.
Primary metabolite levels during pepper development and ripening. Time points presented are 14, 20, 34, 51, 52, 53, 55, 57, 62, and 68 DAP. Data are normalized to the mean response calculated to the 14-DAP stage (value= 1). Values presented are means ± se of three replicates. Asterisks denote differences that were determined to be significant by Student’s t test analysis (P < 0.05) compared with the 14-DAP stage.
- Figure 3.
Networks from the primary metabolite data set of tomato and pepper fruits. Networks were obtained by determining the significant correlations of the metabolite profiles from tomato (A) and pepper (B), guaranteeing a FDR of 0.05. Positive correlations are indicated with red edges, while negative correlations are displayed with blue edges. The gray edges denote the relation between the communities (clusters) of metabolites in the network. The color coding of the nodes, representing the metabolites, denotes the following compound classes: amino acids (red), organic acids (light blue), sugars and sugar alcohols (dark blue), and others (green).
- Figure 4.
Functional distribution of expressed genes. Functional distribution is given for all genes showing significant (P < 0.05) expression values based on MapMan classification (Usadel et al., 2005) in pepper developmental and ripening stages (14, 20, 34, 51, 52 [breaker], 53, 55, 57, 62, and 68 DAP).
- Figure 5.
Expression analysis of pepper development and ripening. A condensed PageMan display of altered pathways is shown. Gene expression data are presented as log2 fold changes in comparison with the first harvested time point (14 DAP). The analyzed time points were 20, 34, 51, 52, 53, 55, 57, 62, and 68 DAP. The data were subjected to a Wilcoxon test in PageMan, and the results are displayed in false color. BINs colored in red are significantly up-regulated, whereas BINs colored in blue are significantly down-regulated.
- Figure 6.
Quantitative PCR of cell wall-, carotenoid-, and ethylene-related genes of tomato and pepper fruits across developmental and ripening stages. Cell wall-related genes were EXP1, EXP3, XTH5, and PG. Carotenoid-related genes were PSY1, PDS, and ZDS. Ethylene-related genes were ACC oxidase (ACO1), ACC synthase (ACS4), and the Nr receptor. The values represent means ± se of four individual plants. Asterisks indicate values determined by t test to be significantly different from the first analyzed stage (P < 0.05).
- Figure 7.
Networks from selected transcripts of tomato and pepper fruits. Transcripts involved in cell wall metabolism, hormone metabolism, redox regulation, major carbohydrate metabolism, protein synthesis, protein targeting, protein posttranslational modification, protein degradation, protein folding, protein assembly, and cofactor ligation were used in the analysis. Color coding for the nodes can be found in Supplemental Figure S2. Transcripts were grouped by functionality on the basis of MapMan gene ontology. Networks were obtained by determining the significant correlations of the transcript profiles from tomato (A) and pepper (B), guaranteeing a FDR of 0.05. Positive correlations are indicated with red edges, while negative correlations are displayed with blue edges. The gray edges denote the relation between the communities (clusters) of metabolites in the network. The color code for the nodes, representing the selected transcripts, corresponds to the MapMan bins and indicates the different function categories.
- Figure 8.
Network-based representation of the integrated metabolomics and transcriptomic data set of tomato and pepper. An analogous procedure to that used to obtain Figures 3 and 7 was employed on the combined data set. Nodes denoting metabolites are drawn in squares, while those representing transcripts are given in circles for tomato (A) and pepper (B). The color coding of nodes represented by circles corresponds to the MapMan bins. The color coding of nodes represented by squares follows that used in Figure 3 for the network of metabolites and that of the nodes represented by circles follows that used in Figure 7 for the network of transcripts. Red edges denote positive correlations, while blue edges represent negative correlations. The gray edges denote the relation between the communities (clusters) of metabolites in the network.
- Figure 9.
Experimental design. To collect pepper (cv Habanero) prior to ripening, fruits were tagged at 14 DAP and harvested at one of the following 11 time points: 14, 20, 26, 34, 51 (breaker−1; Br−1), 52 (breaker; Br), 53 (breaker+1; Br+1), 55 (breaker+2; Br+2), 57 (breaker+5; Br+5), 62 (breaker+10; Br+10), and 68 DAP (breaker+16; Br+16). For tomato (cv Ailsa Craig), the analyzed time points were 7, 17, 27, 39 (mature green [MG]), 41 (breaker−1; Br−1), 42 (breaker; Br), 43 (breaker+1; Br+1), 47 (breaker+5; Br+5), 52 (breaker+10; Br+10), and 57 DAP (breaker+15; Br+15).
Tables
- Table I. Average correlations between gene function categories and compound classes in the integrated networks for pepper and tomato
NA indicates that no significant correlations were observed for the particular pair of gene function category and compound class. The included values indicate that sugars and sugar alcohols are in general more negatively correlated to transcripts involved in starch synthesis in pepper compared with tomato, resulting in a smaller value for the average correlation compared with the used threshold of 0.843. Analogous reasoning implies that organic acids, on the other hand, are more positively correlated to transcripts involved in protein degradation in pepper compared with tomato.
Compound Starch Synthesis Starch Degradation Cell Wall Precursor Synthesis Cell Wall Cellulose Synthesis Protein Synthesis Protein Degradation Pepper Amino acids −0.735 −0.739 NA NA −0.570 0.864 Organic acids −0.765 −0.852 NA NA −0.640 0.355 Sugars and sugar alcohols 0.317 NA NA NA 0.293 0.784 Tomato Amino acids NA NA −0.969 NA NA 0.969 Organic acids NA NA NA NA NA 0.001 Sugars and sugar alcohols 0.968 NA NA NA NA NA
Supplemental Data
Supplemental Figure, Table, and Online Data
Files in this Data Supplement:
- Supplemental Data - Supplemental Figure
- Supplemental Data - Supplemental Table
- Supplemental Data - Supplemental Legends and Supplemental Online Data Link
- Supplemental Data - Supplemental Figure 2
