First genome sequence of a European Alternaria brassicae isolate and genes involved in early development of alternaria leaf spot on Brassica juncea

BACKGROUND: Alternaria brassicae is a necrotrophic fungal pathogen causing grey leaf spot disease in Brassicaceae crops, notably Brassica juncea. While previous genomic studies have focused on Indian isolates, the molecular basis of host–pathogen interactions in European isolates remains unexplored. RESULTS: We report the first genome sequence of a UK A. brassicae isolate (AA1/5), assembled using PacBio and Illumina platforms, revealing a 32.6 Mb genome with 7228 predicted genes. Comparative analysis with the Indian J3 isolate suggests genomic divergence, including fewer repetitive elements and secreted proteins in AA1/5. Dual RNA-sequencing profiling of AA1/5 and two B. juncea cultivars (Sej-2 (2) and Pusa Jaikisan) identified differential expression of fungal genes involved in carbohydrate metabolism, cell wall degradation, and endocytosis. Host transcriptomics revealed suppression of photosystem genes and induction of oxidative pentose phosphate pathway genes. Cultivar-specific responses included differential regulation of defence-related genes such as PR-3, RLP35, JOX4, and CYP81F3. Quantitative reverse transcriptase-PCR validated the host transcriptomic dataset with up-regulation after fungal infection in both cultivars of two pathogenesis-related genes, PR-4 and PR-5. CONCLUSION: This study provides novel insights into the genomic and transcriptomic landscape of a European A. brassicae isolate and its interaction with B. juncea. The findings highlight conserved and divergent pathogenicity mechanisms and host responses, offering a foundation for future resistance breeding and functional studies in Brassicaceae crops.