Abstract
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
7,228 predicted genes. Comparative analysis with the Indian J3 isolate suggests
genomic divergence, including fewer repetitive elements and secreted proteins in
AA1/5. Dual RNA-seq 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 defencerelated genes such as PR-3, RLP35, JOX4, and CYP81F3. Quantitative reverse
transcriptase-PCR validated the host transcriptomic dataset with upregulation 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.
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
7,228 predicted genes. Comparative analysis with the Indian J3 isolate suggests
genomic divergence, including fewer repetitive elements and secreted proteins in
AA1/5. Dual RNA-seq 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 defencerelated genes such as PR-3, RLP35, JOX4, and CYP81F3. Quantitative reverse
transcriptase-PCR validated the host transcriptomic dataset with upregulation 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.
| Original language | English |
|---|---|
| Journal | Pest Management Science |
| Publication status | Accepted/In press - 9 Dec 2025 |