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ARS Home » Pacific West Area » Davis, California » Crops Pathology and Genetics Research » Research » Publications at this Location » Publication #432345
Research Project: Improved Pest and Disease Control for Enhanced Woody Perennial Tree Crop and Grapevine Production

Location: Crops Pathology and Genetics Research

Title: Draft genome sequence of the almond red leaf blotch pathogen Polystigma amygdalinum assembled from infected almond leaves collected in California, USA

Author
item Kasuga, Takao
item Arredondo Sr, Felipe
item TRAVADON, RENAUD - University Of California, Davis
item MAGUVU, TAWANDA - University Of California, Davis
item HERNANDEZ-ROSAS, ALEJANDRO - University Of California, Davis
item TROUILLAS, FLORENT - University Of California, Davis

Submitted to: Microbiology Resource Announcements
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/16/2026
Publication Date: 8/6/2026
Citation: Kasuga, T., Arredondo Sr, F.D., Travadon, R., Maguvu, T., Hernandez-Rosas, A., Trouillas, F. 2026. Draft genome sequence of the almond red leaf blotch pathogen Polystigma amygdalinum assembled from infected almond leaves collected in California, USA. Microbiology Resource Announcements. Volume 15, Issue 9, e00316-26. https://doi.org/10.1128/mra.00316-26.
DOI: https://doi.org/10.1128/mra.00316-26

Interpretive Summary: We generated a first draft of the genome of Polystigma amygdalinum, the fungus that causes red leaf blotch disease in almond trees. Because this organism lives inside plant tissue and is difficult to isolate on its own, DNA was extracted directly from infected almond leaves and sequenced. DNA from the almond plant was then removed using computational methods so that only the fungal genetic material remained. The resulting genome is relatively large for this type of fungus and contains many repeated DNA sequences. This new genetic resource will help scientists compare strains, track how the disease spreads, and develop better tools to detect and manage this emerging pathogen affecting almond production. This work supports key agricultural priorities by helping protect crop productivity and farm profitability, supporting rural economies that depend on almond production, and enabling earlier detection and improved disease management. By strengthening our ability to respond to emerging plant diseases, it also contributes to agricultural market stability, land productivity, and long-term food system resilience.

Technical Abstract: We report a draft genome assembly of Polystigma amygdalinum, the causal agent of almond red leaf blotch. DNA extracted from infected leaves was sequenced using PacBio HiFi, and host-derived reads were removed bioinformatically. The 238.7-Mb assembly (90.8% BUSCO completeness) is highly repetitive (82.3%) and unusually large for an ascomycete.