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

## TL;DR

This study provides a high-quality genome assembly of an Indian Plasmopara viticola isolate and reveals molecular mechanisms involved in its interaction with grapevine.

## Contribution

The first high-quality genome assembly of an Indian P. viticola isolate and insights into its pathogenicity and host interaction mechanisms.

## Key findings

- The PV01 isolate genome encodes 12,404 predicted protein-coding genes and diverse effectors involved in host manipulation.
- Dual RNA-seq analysis showed suppression of photosynthesis and activation of defense pathways in grapevine during infection.
- P. viticola exhibited infection-stage-specific expression of effectors and genes related to autophagy suppression and redox homeostasis.

## Abstract

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.