Fig. 2

Identification of hub genes in plant responses to N-acyl homoserine lactones. Integrated data set containing 19,085 differentially expressed genes in 20 samples, collected from whole seedlings, 72 h post-treatment with different AHL molecules including C6-HSL (C06), oxo-C10-HSL (C10), oxo-C14-HSL (C14), and AHL mix (MIX) (Schenk et al. 2014; Shrestha et al. 2022; Duan et al. 2023), was used to perform weighted gene co-expression network analysis (A). This analysis revealed the relationships (A) between AHL (trait) and gene clusters (module), the number of genes for each module was presented in a barplot (B). Hub genes were identified using thresholds (|gene significance| > 0.4 and |module membership| > 0.8) from five modules, significantly correlating with the AHL treatment or the solvent control (CTL), (p value < 0.05). Hub gene sets identified in five modules (MEblue, MEgreen, MEred, MEturquoise, and MEyellow) were termed blueCTL, greenmix, redC10, turquoisemix, and yellowmix, respectively (C)