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Background   Valsa  canker is a serious disease in the stem of  Malus sieversii , caused by  Valsa mali . However, little is known about the global response mechanism in  M. sieversii  to  V. mali  infection.    Results  Phytohormone jasmonic acid (JA) and salicylic acid (SA) profiles and transcriptome analysis were used to elaborate on the dynamic response mechanism. We determined that the JA was initially produced to respond to the necrotrophic pathogen  V. mali  infection at the early response stage, then get synergistically transduced with SA to respond at the late response stage. Furthermore, we adopted Pacific Biosciences (PacBio) full-length sequencing to identify differentially expressed transcripts (DETs) during the canker response stage. We obtained 52,538 full-length transcripts, of which 8139 were DETs. Total 1336 lncRNAs, 23,737 alternative polyadenylation (APA) sites and 3780 putative transcription factors (TFs) were identified. Additionally, functional annotation analysis of DETs indicated that the wild apple response to the infection of  V. mali  involves plant-pathogen interaction, plant hormone signal transduction, flavonoid biosynthesis, and phenylpropanoid biosynthesis. The co-expression network of the differentially expressed TFs revealed 264 candidate TF transcripts. Among these candidates, the WRKY family was the most abundant. The  MsWRKY7  and  MsWRKY33  were highly correlated at the early response stage, and  MsWRKY6 ,  MsWRKY7 ,  MsWRKY19 ,  MsWRKY33 ,  MsWRKY40 ,  MsWRKY45 ,  MsWRKY51 ,  MsWRKY61 ,  MsWRKY75  were highly correlated at the late stage.    Conclusions  The full-length transcriptomic analysis revealed a series of immune responsive events in  M. sieversii  in response to  V. mali  infection. The phytohormone signal pathway regulatory played an important role in the response stage. Additionally, the enriched disease resistance pathways and differentially expressed TFs dynamics collectively contributed to the immune response. This study provides valuable insights into a dynamic response in  M. sieversii  upon the necrotrophic pathogen  V. mali  infection, facilitates understanding of response mechanisms to canker disease for apple, and provides supports in the identification of potential resistance genes in  M. sieversii .    Supplementary Information  The online version contains supplementary material available at 10.1186/s12864-021-07366-y.

PacBio full-length transcriptome of wild apple (Malus sieversii) provides insights into canker disease dynamic response