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Updated: Jun 16, 2026

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

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Complete genomes of grapevine downy mildew reveal effector cluster evolution driven by complex structural variations.

Lianzhu Zhou¹, Shaowei Cui¹, Hao Zhang¹

¹State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.

Horticulture Research

|June 15, 2026

Summary

The genome of grapevine downy mildew (Plasmopara viticola) is highly dynamic, with structural variations and gene duplications driving effector diversification and pathogenicity. This study reveals key genomic features underlying intraspecific variation in this important grapevine pathogen.

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Area of Science:

Plant Pathology
Genomics
Molecular Biology

Background:

Plasmopara viticola causes grapevine downy mildew, a significant agricultural disease.
Intraspecific variation in pathogenicity and genetic diversity of P. viticola is substantial.
Genomic underpinnings of this variation are not fully understood.

Purpose of the Study:

To characterize the genomic features contributing to intraspecific variation in Plasmopara viticola.
To perform comparative genomics of two P. viticola isolates from different Vitis species.

Main Methods:

PacBio HiFi sequencing was used to assemble two P. viticola genomes (PvH and PvS).
Comparative genomic analysis was conducted on the assembled genomes.
Identification and characterization of putative effectors, including CRNs, RxLRs, and CAZymes.

Main Results:

Two complete 17-chromosome genome assemblies of P. viticola were generated (PvH: 115.3 Mb; PvS: 113.0 Mb).
Nearly 90% of putative effectors are organized in local duplicated gene clusters.
Structural variations (SVs), including duplications and inversions, are hotspots for effector diversification, with PvH showing increased CRNs and strain-specific effectors.

Conclusions:

The genome architecture of P. viticola is highly dynamic, with SVs and local gene duplication driving effector evolution.
This study provides a genome-resolved framework for understanding intraspecific genomic diversity in P. viticola.
Findings lay the groundwork for future population-level and functional studies of grapevine downy mildew.