Fig. 4

Profile of differentially expressed genes (DEGs) between the green- and red-colored berry stages of S. chinensis. a. Fruit shape at 40 (green-colored berry) and 120 (red-colored fruit berry) days after flowering (DAF) in S. chinensis. b. Gene ontology (GO) enrichment for DEGs between 40 DAF and 120 DAF. The GO enrichment analysis for up- (904 genes) and down- (921 genes) regulated genes at 120 DAF (left panel in Figure) was performed by using DAVID according to an EASE score < 0.001, and significant, uniquely represented GO terms were then selected. c. Activation of the phenylpropanoid biosynthetic pathway to coniferyl alcohol at 120 DAF and identification of the corresponding unigenes. d. Mapping to genes in the phenylpropanoid biosynthetic process to other closely related biosynthetic processes, including lignin, suberin, flavonoid, proanthocyanidin, phenol-containing compound, cinnamic acid, karrikin, and cell wall biosynthetic processes. e. Identification of DEGs related to lignan biosynthetic pathways at 40 and 120 DAF. f. Transcriptional network among genes upregulated at 120 DAF related to phenylpropanoid biosynthesis and the responses to ABA, JA, ethylene, and hydrogen peroxide. After selecting up-regulated genes enriched in those five GO terms, the interaction between those genes was identified by using STRING and further analyzed using Cytoscape on the basis of the degree of connectivity of the nodes. In the network, the interaction between genes in ‘phenylpropanoid biosynthetic process’ and other functional terms, including ‘responses to ABA’, ‘JA mediated signaling’, ‘ethylene-activated signaling’, or ‘response to hydrogen peroxide’, are indicated with red-color dot line. In addition, genes in phenylpropanoid pathway are indicated with orange-color letter