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

Abstract

Background Cytospora canker is a serious disease in the stem of Malus sieversii, caused by Cytospora mali. However, little is known about the global response mechanism in M. sieversii to C. 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 C. 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 8,139 were DETs. Total 1,336 lncRNAs, 23,737 alternative polyadenylation (APA) sites and 3,780 putative transcription factors (TFs) were identified. Additionally, functional annotation analysis of DETs indicated that the wild apple response to the infection of C. 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 C. 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 C. 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.

Genome-wide characterization of the chitinase gene family in wild apple (Malus sieversii) and domesticated apple (Malus domestica) reveals its role in resistance to Valsa mali

“…The relative transcript abundance of the chitinase genes was analyzed with the 2 −ΔΔ C t method ( Livak and Schmittgen, 2001 ). The EF-1α (Elongation factor 1-α) gene has been evaluated for internal reference in apple species ( Zhu et al., 2019 ) and served as reference in our previous work ( Liu et al., 2021 ; Haxim et al., 2021 ; Liu et al., 2021 ) because of its stable expression in our previous work under V.mali infection. Therefore, the EF-1α gene was also used as an internal reference for the qPCR quantification in the present study.…”

“…Transcriptome data for M. sieversii (NCBI BioProject: PRJNA687214) ( Liu et al., 2021 ) and M. domestica (NCBI SRA accession: SRP034726) ( Yin et al., 2016 ) in response to V. mali infection were used to analyze differentially expressed genes. The fragments per kilobase of transcript per million fragments mapped (FPKM) value was calculated for each gene.…”

“…The mining of candidate genes and development of disease-resistant cultivars are effective and practical approaches to control the disease. The transcriptomic changes in response to V. mali infection have been investigated previously in M. sieversii ( Liu et al., 2021 ) and M. domestica ( Yin et al., 2016 ). The plant–pathogen interaction, plant hormone signal transduction, flavonoid biosynthesis, and phenylpropanoid biosynthesis pathways of M. sieversii ( Haxim et al., 2021 ; Liu et al., 2021 ), and chitin signaling pathway of M. domestica ( Yin et al., 2016 ) were significantly enriched in response to infection by V. mali.…”

“…The transcriptomic changes in response to V. mali infection have been investigated previously in M. sieversii ( Liu et al., 2021 ) and M. domestica ( Yin et al., 2016 ). The plant–pathogen interaction, plant hormone signal transduction, flavonoid biosynthesis, and phenylpropanoid biosynthesis pathways of M. sieversii ( Haxim et al., 2021 ; Liu et al., 2021 ), and chitin signaling pathway of M. domestica ( Yin et al., 2016 ) were significantly enriched in response to infection by V. mali. Exploration of the disease-resistance genes in apple responsive to V. mali infection is important for disease prevention in domesticated and wild apple species, especially M. sieversii .…”