Fig. 1: Analysis of mobile mRNAs between rootstock and scion under 6-hour chilling conditions.

a Number and direction of mobile mRNAs exchanged between cucumber (Csa) scion and pumpkin (Cmo) rootstock under chilling stress. Move-down Csa mRNAs and move-up Cmo mRNAs are indicated by red letters. b KEGG enriched pathway analysis of 80 move-up Cmo mRNAs induced by cold stress. The red letters indicate the BCAA (Valine, leucine, and isoleucine) biosynthesis pathway, while the blue letters on the graphs represent the proportion of gene numbers and p-value. KEGG enrichment analyses were performed using Fisher’s exact test (p < 0.05) and corrected for multiple comparisons by false discovery rate (FDR). c KEGG enriched pathway analysis of 174 CsaDIMs (differential intensity of metabolites) in the Csa scion of Csa/Cmo grafts under chilling stress compared to normal conditions. The red letters indicate the BCAA biosynthesis pathway, and the blue letters on the graphs represent the proportion of metabolite numbers and P-value. KEGG enrichment analyses were performed using Fisher’s exact test (p < 0.05) and corrected for multiple comparisons by false discovery rate (FDR). d Normalized fold change of CsaDIMs in the Csa scion of Csa/Csa and Csa/Cmo under chilling stress compared to the same tissue under normal conditions. The square red-to-blue colored block indicates the normalized fold changes compared to Csa scion of Csa/Csa under normal conditions. e Networks of chilling-induced Cmo and Csa mobile mRNAs, Csa DEGs involved in the metabolites L-leucine, L-valine, and L-isoleucine biosynthesis. Red circles indicate the four metabolites, grey ones indicate Csa DEGs, blue circles indicate Csa mobile mRNAs, and orange ones indicate Csa DEG-coordinated homologous Cmo mobile mRNAs. Arrows (red for positive and blue for negative) indicate the correlation between metabolites and Csa DEGs. The correlation analysis was conducted using Pearson correlation coefficients (|cor| ≥ 0.95, P-value < 0.05, two-sided). Source data are provided as a Source Data file. f Schematic showing mRNA mobility in the BCAA biosynthesis pathway in Csa/Cmo grafts.