Bursaphelenchus xylophilus is a pine wood nematode capable of destroying pine forests. Exploring the genes providing resistance to this pathogen and understanding their resistance mechanisms is thus necessary and constitutes an effective way to tackle this problem. We used Pinus tabuliformis Carriere to dissect its response to B. xylophilus strain BxFC. The 30 d inoculation results showed that the P. tabuliformis germplasms exhibited a wide resistance spectrum. Some lines were sensitive with the needles fully wilted and the MDA content and the relative conductivity of needles greatly increased, while some lines demonstrated strong resistance with good needle vigor and better physiological conditions. Moreover, the transcriptome analysis revealed 7928 differentially expressed genes (DEGs) between the resistant and sensitive germplasm pools, including 3754 upregulated and 4174 downregulated genes in the resistant lines. These DEGs were specially enriched in the pathways of plant–pathogen interaction (318 genes), phenylpropanoid biosynthesis (108 genes), ubiquitin-mediated proteolysis (47 genes), carotenoid biosynthesis (18 genes), and monoterpenoid biosynthesis (9 genes). Accordingly, P. tabuliformis utilized multiple ways to control the proliferation and activity of B. xylophilus, such as immune response, ubiquitination, thickening plant cell walls, and increasing its terpenoid and antioxidant contents. Our results could thus help in better understanding the resistance process of P. tabuliformis against B. xylophilus and offer some new strategies and gene resources for a molecular breeding program of resistant P. tabuliformis.

Zelkova schneideriana Hand.-Mazz. is an ecologically and economically valuable tree species in China, but its sensitivity to low temperature restricts its use in colder regions. To identify genes and pathways associated with chilling responses, we combined physiological screening, full-length transcriptome construction, Illumina RNA-seq, and time-ordered gene co-expression network analysis (TO-GCN). Fifty seedling lines were evaluated after 7 d at 4 °C, and the line with the lowest relative electrolyte leakage (REL) and malondialdehyde (MDA) content was selected for transcriptome profiling at 0, 3, and 6 d of chilling treatment. RNA-seq detected 5875 differentially expressed genes. Most expression changes occurred by day 3 and were largely maintained on day 6. Pathway reconstruction showed contrasting dynamics between antioxidant-related systems: Flavonoid and anthocyanin biosynthesis were progressively activated, whereas glutathione-related genes, particularly glutathione S-transferase family members, were broadly repressed. TO-GCN highlighted ZeF3H (Ze_transcript_14112) as a late-stage hub associated with anthocyanin biosynthesis and ZeDRT102 (Ze_transcript_44427) as an early-stage hub linked to DNA damage repair and glutathione-associated genes. These results indicate that the chilling response in Z. schneideriana involves activation of flavonoid-based protection together with weakened glutathione-mediated redox regulation, providing candidate genes for functional validation and cold-resistance breeding. These insights provide a critical foundation for molecular breeding strategies that will ultimately facilitate the successful introduction and stable cultivation of this valuable species in northern temperate climates.