Temporal transcriptomics provides insights into host‒pathogen interactions: a case study of Didymella pinodella and disease-resistant and disease-susceptible pea varieties.

Ascochyta blight is a fungal disease affecting peas, causing significant damage to the plant and reducing crop yield. Host‒pathogen interactions can inform disease prevention and control strategies but remain poorly understood. Here, we generate a near-chromosome-level assembly for Didymella pinodella HNA18, a pathogenic fungus that causes pea ascochyta blight. Comparative genomic analysis of D. pinodella HNA18 and seven publicly available Didymella genomes revealed that the genome of D. pinodella HNA18 encodes the most conserved biosynthetic gene clusters (BGCs) and a similar number of carbohydrate-activating enzyme (CAZyme) genes compared to other Didymella species. Furthermore, by sequencing and analyzing the transcriptomic data of D. pinodella HNA18 and disease-susceptible and disease-resistant pea varieties during the infection process, we found that the pathogenic fungus mobilized a similar set of infection genes to attack the disease-susceptible and disease-resistant pea varieties, but the timing and intensity of these infection genes were different. For pea varieties in response to the pathogenic fungus, disease-susceptible and disease-resistant pea varieties mobilized similar types of defense genes, while the disease-resistant pea used a higher number of defense genes relative to the disease-susceptible pea during the entire infection process. This study not only provides multiomic resources for the study of the pathogenic fungus D. pinodella HNA18 against its disease-susceptible and disease-resistant pea varieties but also deciphers the mode of interaction between pathogenic fungal infection and plant defense.