Fig 1.
Physiological and morphological changes during sweet cherry (Prunus avium L. cv. ‘Black Pearl’) fruit development.
(A) Photos of developmental stages. (B) Fruit firmness (N). (C) Changes in total soluble solids (TSS). (D) Changes in a*/b* ratio. Error bars in (B), (C), (D) represent ± SE from 10 replicates. (E) Anthocyanin content at different developmental stages. Error bars represent ± SE from three replicates. Tukey’s test significant at p < 0.05, indicated by a, b, c, and d.
Fig 2.
Dynamic metabolome of sweet cherry development and ripening.
(A) Principal component analysis (PCA) of metabolites identified in developmental stages. (B) Heatmap of all differentially expressed metabolites (DEMs) at four developmental stages. Color indicates level of relative content of each DEM, from green (low) to red (high). (C) Clustering analysis of all DEMs according to their variation tendency, and (D) metabolite variation tendencies among the 9 cluster profiles.
Fig 3.
Differentially accumulated metabolites in sweet cherry at different fruit development stages.
(A) Volcano plots of differential metabolites in 10 vs. 25 DAFB, 25 vs. 33 DAFB, and 33 vs. 40 DAFB, respectively. (B) Venn diagram of DEMs in 10 vs. 25 DAFB, 25 vs. 33 DAFB, and 33 vs. 40 DAFB. (C) Heatmap of 49 DEMs obtained from intersection of 10 vs. 25 DAFB, 25 vs. 33 DAFB, and 33 vs. 40 DAFB.
Table 1.
The profile of the 49 common metabolites.
Fig 4.
KEGG pathway enrichment analysis of DEMs in (A) 10 vs. 25 DAFB, (B) 25 vs. 33 DAFB, and (C) 33 vs. 40 DAFB. Heatmaps of top 10 DEMs in (D) 10 vs. 25 DAFB, (E) 25 vs. 33 DAFB, (F) 33 vs. 40 DAFB, and (G) 10 vs. 40 DAFB.
Fig 5.
Correlation analysis of metabolomic and transcriptomic data.
(A) PCA plots of differentially expressed genes (DEGs) identified from different developmental stages of sweet cherry. (B) Number of DEGs among different fruit-development stages. (C) Heatmap of all identified DEGs at four stages. Red and green indicate increased and decreased gene transcript levels, respectively. (D) Nine-quadrant diagrams show the correlation of compounds (obtained from metabolomic analysis) and genes (identified from RNA-seq) in sweet cherry. Blue, green, red, and black points indicate DEGs and DEMs pairs, non-DEGs and DEM pairs, DEGs and non-DEM pairs, and non-DEGs and non-DEM pairs, respectively. (E-H) Association analysis of transcriptomic and metabolomic variation. Connection network between top 10 DEMs and screened DEGs (|log2FoldChange| > 1, p < 0.05, and FPKM > 10) in (E) 10 vs. 25 DAFB, (F) 25 vs. 33 DAFB, (G) 33 vs. 40 DAFB, and (H) 10 vs. 40 DAFB. Red and green ovals in nodes represent DEMs and DEGs, respectively. Edges represent “relationships” between any DEMs and DEGs, yellow and gray represent positive and negative correlations, respectively, as determined by absolute value of |r| > 0.90.
Fig 6.
Expression profiles of DEGs and DEMs associated with (A) sugar metabolism, (B) organic acid metabolism, and (C) flavonoid metabolism.