Dual species dynamic transcripts reveal the interaction mechanisms between Chrysanthemum morifolium and Alternaria alternata

Abstract

Background Chrysanthemum (C. morifolium) black spot disease caused by Alternaria alternata is one of the plant’s most destructive diseases. Dual RNA-seq was performed to simultaneously assess their transcriptomes to analyze the potential interaction mechanism between the two species, i.e., host and pathogen. Results C. morifolium and A. alternata were subjected to dual RNA-seq at 1, 12, and 24 hours after inoculation, and differential expression genes (DEGs) in both species were identified. This analysis confirmed 153,532 DEGs in chrysanthemum and 14,932 DEGs in A. alternata, that were involved in plant-fungal interactions and phytohormone signaling. Fungal DEGs such as toxin synthesis related enzyme and cell wall degrading enzyme genes played important roles during chrysanthemum infecton. Moreover, a series of key genes highly correlated with the early, middle, or late infection stage was identified, together with the regulatory network of key genes annotated in PRG or PPI databases. Highly correlated genes were identified at the late infection stage, expanding our understanding of the interplay between C. morifolium and A. alternata. Additionally, six DEGs each from chrysanthemum and A. alternata were selected for qRT-PCR assays to validate the RNA-seq output. Conclusions Collectively, data obtained in this study enriches the resources available for research into the interactions that exist between chrysanthemum and A. alternata, thereby providing a theoretical basis for the development of new chrysanthemum varieties with resistance to pathogen.