Combining whole genome and transcriptome sequencing to analyze the pathogenic mechanism of <i>Diplodia sapinea</i> blight in <i>Pinus sylvestris</i> var. <i>mongolica</i> Litv.

<i>Diplodia sapinea</i> (= <i>Sphaeropsis sapinea</i>) is an opportunistic pathogen that usually lives in symbiosis (the coexistence of dissimilar organisms) with its host and can cause disease under extreme climatic or physiological stress. In this study, we generated a high-quality genome map of <i>D. sapinea</i> using PacBio Circular Consensus Sequencing (CCS) technology and analysed the key disease-causing genes of <i>D. sapinea</i> by RNA sequencing (RNA-seq). In the study, a number of cell wall degrading enzyme genes were identified to be up-regulated during pathogen infection, which may be involved in biotic stress response in <i>P. sylvestris</i> var. <i>mongolica</i> Litv. It was also found that the expression of antioxidant-related genes, such as those involved in carotenoid biosynthesis, ascorbate and glutathione metabolism, was up-regulated in the <i>P. s</i>. var. <i>mongolica</i> Litv. after fungus infection. Differently expressed genes (DEGs) -based protein-protein interaction (PPI) network was constructed that included 163 pairs of significantly positively correlated proteins, forming three highly interacting gene clusters, and the PPI network was predicted to be associated with the replication and propagation processes of the fungus. These results provide important information for understanding the pathogenic mechanisms of <i>Diplodia</i> tip blight and developing control strategies in <i>P. s</i>. var. <i>mongolica</i> Litv.