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ORIGINAL RESEARCH article

Front. Plant Sci.

Sec. Plant Pathogen Interactions

This article is part of the Research TopicAdvances in Genomics of Plant Pathogens and Host-Pathogen InteractionView all 9 articles

Genome and Transcriptome Analyses Reveal Molecular Mechanisms Underlying the Interaction between Plasmopara viticola and Grapevine

Provisionally accepted
R. KaranR. Karan1M K PrasannaKumarM K PrasannaKumar1*Kiran B MKiran B M1J HarishJ Harish1B. RoopashreeB. Roopashree1Gopal VenkateshbabuGopal Venkateshbabu1Dr. Swathi S. PatilDr. Swathi S. Patil1S. ShreedevasenaS. Shreedevasena2Pramesh DevannaPramesh Devanna3Manjunatha C.Manjunatha C.4Aditya KukretiAditya Kukreti4Aditya Narayan SarangiAditya Narayan Sarangi5Raju SoolanayakanahallyRaju Soolanayakanahally6Sateesh KagaleSateesh Kagale7
  • 1University of Agricultural Sciences, Bangalore, Bangalore, India
  • 2ICAR - Directorate of Medicinal and Aromatic Plants Research, Anand, India
  • 3ICAR - Directorate of Mushroom Research, Solan, India
  • 4National Bureau of Agricultural Insect Resources, Bengaluru, India
  • 5Basesolve Informatics Pvt Ltd, Ahmedabad, India
  • 6Saskatoon Research and Development Centre, Saskatoon, Canada
  • 7National Research Council Canada Aquatic and Crop Resource Development Research Centre, Ottawa, Canada

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Plasmopara viticola, an obligate biotrophic oomycete, is the causal agent of downy mildew in grapevine (Vitis vinifera) and a major constraint to viticulture worldwide. Here, we report the first high-quality whole-genome assembly of an Indian P. viticola 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 P. viticola 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, P. viticola 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 P. viticola pathogenicity and grapevine immune modulation.Key words: Grapes, Downy mildew, Genome, Transcriptome, Effectors

Keywords: Downy mildew, Effectors, Genome, grapes, grapevine, Plasmopara viticola, Transcriptome

Received: 10 Dec 2025; Accepted: 16 Feb 2026.

Copyright: © 2026 Karan, PrasannaKumar, M, Harish, Roopashree, Venkateshbabu, Patil, Shreedevasena, Devanna, C., Kukreti, Sarangi, Soolanayakanahally and Kagale. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: M K PrasannaKumar

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Supplementary Material