Endophytic fungi enhance plant growth and stress resilience, yet their molecular roles in the roots of the endangered tree Phoebe bournei 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 Rhizophagus irregularis 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 PbMPK3, PbCML42, PbCML41.2, and PbGSTU28, 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 P. bournei. 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.

The Sugars Will Eventually be Exported Transporters (SWEET) family plays a crucial role in the carbohydrate distribution, phloem loading, and stress response of plants, yet the evolutionary characteristics and functional diversification of SWEET genes in the endangered timber species Phoebe bournei (Hemsl.) Yen C. Yang remain largely unexplored. In this study, 21 PbSWEET genes were identified and classified into four subfamilies (A–D). Subfamily A exhibited a unique lineage expansion, mainly driven by tandem and segmental duplications. The nonsynonymous-to-synonymous substitution ratio (Ka/Ks) values of all duplicate gene pairs were all less than 1, indicating a strong selective suppression effect; consistent with this evolutionary constraint, the majority of PbSWEET proteins harbor the conserved Medicago truncatula Nodulin 3/saliva (MtN3_slv) domain, with only a few exceptions lacking a complete version. Promoter and hormone response analyses revealed that under abscisic acid (ABA) stress, PbSWEET4 exhibited an immediate burst, whereas PbSWEET10 showed a delayed burst. Physiological data indicated that soluble sugars may be more dominant osmolytes than proline (Pro), a pattern that points to a potential carbon-centric regulatory strategy. PbSWEET4 showed an early burst before sugar/oxidative peaks, suggesting a possible non-canonical signaling role, whereas PbSWEET10 exhibited a late increase coinciding with sugar/malondialdehyde (MDA) peaks, suggesting potential involvement in sugar redistribution. Under methyl jasmonate (MeJA) treatment, PbSWEET10 was rapidly induced, yet sugar accumulation occurred only at 24 h, a temporal decoupling that suggests a possible transcription–metabolism decoupling. Collectively, these correlative patterns point to a possible dual-wave transcriptional mechanism and nominate PbSWEET10 as a candidate for stress response, though these inferences require functional validation.