Nificantly various from that of CK at 5 dpi, even though the expression of those genes was upregulated at other time points, in particular at two dpi; additionally, the expression of those genes was upregulated at all time points in P. massoniana (Figure 6a,b). Their expression levels at diverse time points have been additional verified by Real-time quantitative PCR (RT-qPCR, Figure 6c,d). The results indicated that these chalcone synthase genes showed no considerable adjust or have been upregulated to a lesser degree than at other time points in P. thunbergii at five dpi.Int. J. Mol. Sci. 2021, 22,9 ofFigure six. Expression patterns of chalcone synthase genes at unique time points. (a) Expression levels for chalcone synthase genes based on per kilobase of exon model per million mapped reads (TPM) in Pinus thunbergii; (b) expression levels for chalcone synthase genes primarily based on TPM in P. massoniana; (c) modifications in expression levels verified by real-time quantitative PCR (RT-qPCR) for chalcone synthase genes in P. thunbergii; (d) modifications in expression levels verified by RT-qPCR for chalcone synthase genes in P. massoniana. The information are provided as the imply or imply with standard deviation.For each of your 5 chalcone synthase genes, genes very correlated with them within the yellow module were screened. The genes in the yellow module whose weight values with chalcone synthase genes had been greater than 0.2 were chosen, and their network information were exported to Cytoscape by Prefuse Force Directed Layout primarily based around the weight values amongst two genes. The whole network contained 163 regulatory relationships of 93 genes (Figure 7a, details could be found in Table S15). Among the 93 genes within the yellow module, 47 had been enriched in 40 diverse pathways (Table S16). Amongst them, most genes have been enriched in metabolic pathways (ko01100) and Eicosapentaenoic acid ethyl ester Epigenetic Reader Domain biosynthesis of secondary Seliciclib MedChemExpress metabolites (ko01110), followed by flavonoid biosynthesis (ko00941). There had been three chalcone synthase genes (No. three, chalcone synthase 1; No. 7, chalcone synthase 3; and No. 15, chalcone synthase four) enriched in flavonoid biosynthesis. The correlation among the enriched pathways was studied, and it was identified that flavonoid biosynthesis was related to metabolic pathways, biosynthesis of secondary metabolites, flavone and flavonol biosynthesis (ko00944), and phenylpropanoid biosynthesis (ko00940, Figure 7b). Consequently, soon after PWN invaded pine trees, its population size was proportional for the expression of many chalcone synthase genes in pine trees, and chalcone synthase genes were mainly involved in flavonoid biosynthesis, which is related to flavone and flavonol biosynthesis, and phenylpropanoid biosynthesis and they may influence the population of PWN in pine trees.Int. J. Mol. Sci. 2021, 22,ten ofFigure 7. Gene network for chalcone synthase genes inside the yellow module. (a) Coexpression network for chalcone synthase genes (weight value 0.2, detailed in Table S15). Prefuse force directed layout was applied primarily based on the weight value between two genes. The size of the nodes represents the gene significance for the nematode population (from 0.3806 to 0.8330). The color of the nodes represents module membership (from -0.8649 to 0.9746). The colors on the lines represent the weight value in between two genes (from 0.2000 to 0.2928). The labels on the nodes are based on intramodular connectivity (from 6.1505 to 56.6806). The chalcone synthase genes are highlighted with red labels; (b) KEGG enrichment network. The nodes represen.
