Identification of Ubiquitin Genes and Their Expression Patterns in Pinus massoniana Under Infection Stress from the Pinewood Nematode

Ubiquitins (Ubs) play a crucial role in plant–pathogen interactions, particularly the RPL40 family, which is essential for protein synthesis. While Pinus massoniana is highly susceptible to pine wilt disease (PWD) caused by Bursaphelenchus xylophilus, the defense mechanisms mediated by RPL40s remain poorly understood. Here, we performed a genome-wide identification of the ubiquitin and ubiquitin-like gene family (PmUBQs) in P. massoniana. We identified 30 PmUBQ genes unevenly distributed across 11 chromosomes, which were classified into six subfamilies based on phylogenetic analysis. An analysis of promoter regions indicated that the PmUBQ genes were enriched with cis-acting elements associated with stress responses, hormone regulation, and development. Specifically, two group II members, PmRPL40-1 and PmRPL40-2, located on chromosomes 12 and 11, respectively, were identified and exhibited distinct responses to B. xylophilus infection in resistant and susceptible P. massoniana. PmRPL40-1 was significantly highly expressed in the 15 days post-inoculation, while PmRPL40-2 was downregulated on day 1 and then upregulated. Moreover, both genes showed peak divergence at 15 days post-inoculation; the expression levels of PmRPL40-1 and PmRPL40-2 in resistant P. massoniana were approximately 1.8- and 3.7-fold higher, respectively, than in susceptible P. massoniana. These patterns suggest that PmRPL40s might be involved in the rapid activation of defense responses and late-stage cell repair. Notably, transient overexpression of PmRPL40-1 in P. massoniana led to a significant 1.6-fold increase in the jasmonic acid (JA) content (p < 0.0001). These findings reveal the key PmUBQ genes and suggest that PmRPL40s contribute to PWD resistance potentially through the modulation of JA signaling, offering potential targets for molecular breeding in P. massoniana.