Transcriptomic Insights into Endophytic Fungus-Mediated Enhancement of Root Growth and Stress Resistance in Phoebe bournei

Endophytic fungi enhance plant growth and stress resilience, yet their molecular roles in the roots of the endangered tree <i>Phoebe bournei</i> remain unclear. A comparative RNA-seq analysis was performed on root transcriptomes from wild, endophyte-colonized adult trees (OT) and axenically grown seedlings (ST). Unmapped reads were analyzed against the NCBI nucleotide (NT) database using BLASTN (v2.17.0), revealing <i>Rhizophagus irregularis</i> as the predominant endophytic fungus. Differential expression analysis identified 5891 DEGs, which were significantly enriched in pathways related to plant-pathogen interactions, phenylpropanoid biosynthesis, plant hormone signal transduction, and MAPK signaling. Key upregulated genes included <i>PbMPK3</i>, <i>PbCML42</i>, <i>PbCML41.2</i>, and <i>PbGSTU28</i>, suggesting enhanced ROS scavenging, calcium signaling, and defense activation. RT-qPCR validation confirmed the transcriptomic trends for selected genes. Our findings reveal that root endophytic fungi modulate a coordinated network involving immune priming, phytohormone regulation, and redox homeostasis, thereby supporting root development and enhancing resistance to biotic and abiotic stresses in <i>P. bournei</i>. This study provides foundational molecular insights into beneficial plant-endophyte interactions and identifies candidate genes that are valuable for the conservation and breeding of this threatened species.