Genome and transcriptome analyses reveal molecular mechanisms underlying the interaction between Plasmopara viticola and grapevine

<i>Plasmopara viticola</i>, an obligate biotrophic oomycete, is the causal agent of downy mildew in grapevine (<i>Vitis vinifera</i>) and a major constraint to viticulture worldwide. Here, we report the first high-quality whole-genome assembly of an Indian <i>P. viticola</i> isolate (PV01), generated using a hybrid sequencing approach combining Illumina and Oxford Nanopore platforms. The assembled genome spans 84.09 Mb across 182 contigs, with an N50 of ~971 kb and 97% BUSCO completeness, and encodes 12,404 predicted protein-coding genes, diverse transposable elements, and lineage-specific expansions. Functional annotation revealed a rich repertoire of effectors, including RXLR, CRN, and apoplastic effectors, as well as putative virulence-associated and secretory proteins likely involved in host manipulation and immune suppression. Comparative ortholog analysis across <i>P. viticola</i> isolates and representative oomycetes identified a conserved core genome alongside 164 PV01-specific orthogroups, reflecting isolate-level diversification. Dual RNA-seq analysis of infected grapevine leaves revealed strong suppression of chloroplast- and photosynthesis-associated pathways in the host, coupled with induction of defense-related genes, including PR proteins, WRKY transcription factors, calcium signaling components, and JA/ET-mediated pathways. Concurrently, <i>P. viticola</i> displayed infection-stage-specific expression of effectors, apoplastic proteases, vesicle trafficking components, and genes associated with autophagy suppression and redox homeostasis. Together, these integrated genomic and transcriptomic analyses provide insights into the molecular mechanisms underlying <i>P. viticola</i> pathogenicity and grapevine immune modulation.