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ARS Home » Northeast Area » Frederick, Maryland » Foreign Disease-Weed Science Research » Research » Publications at this Location » Publication #431238
Research Project: Integrative Genomic and Biological Approaches to Detect and Manage Emerging Foreign Fungal and Oomycete Plant Pathogens

Location: Foreign Disease-Weed Science Research

Title: Comparative genomics and in planta transcriptomics elucidate the genetic arsenal used by boxwood blight pathogen Calonectria henricotiae

Author
item Dobbs, John
item Shishkoff, Nina
item Crouch, Joanne

Submitted to: PhytoFrontiers
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/12/2026
Publication Date: 5/18/2026
Citation: Dobbs, J.T., Shishkoff, N., Crouch, J. 2026. Comparative genomics and in planta transcriptomics elucidate the genetic arsenal used by boxwood blight pathogen Calonectria henricotiae. PhytoFrontiers. https://doi.org/10.1094/PHYTOFR-04-26-0044-FI.
DOI: https://doi.org/10.1094/PHYTOFR-04-26-0044-FI

Interpretive Summary: Boxwood blight is a foreign plant disease that recently invaded the United States and threatens the health of boxwood, a foundational plant in ornamental landscaping and nursery production, valued at over $100 million annually. The disease is caused by two closely related fungal pathogens, one of which is more aggressive, heat tolerant, and more resistant to fungicides, though not yet present in the U.S. To understand what drives these differences, researchers compared the pathogens' genetic makeup and infection behavior. They found that the more aggressive foreign species carries a broader set of genes linked to plant infection, heat survival, and treatment resistance. These findings are critical for strengthening biosecurity, guiding early detection and regulatory decisions, and shaping future disease management, especially for those working to protect plant health, trade, and the nursery economy.

Technical Abstract: Boxwood blight is a devastating fungal disease causing significant economic losses to the nursery industry and damaging established landscapes. The European pathogen, Calonectria henricotiae (Che), is more aggressive, heat-tolerant, and less sensitive to fungicides than its globally widespread counterpart, C. pseudonaviculata (Cps). However, the genetic underpinnings for these phenotypic differences are not well understood. We conducted a comparative genomic analysis of 10 Che and 69 Cps isolates and generated the first in planta transcriptomic dataset for these pathogens. Analysis of inoculated tissue revealed 5,073 differentially expressed genes (DEGs). While many DEGs were shared (3,124), the representative Che isolate expressed a larger (1,038 vs. 908 significantly upregulated in planta [UIP] genes) and more diverse (896 vs. 70 characterized genes) unique UIP genes than the representative Cps isolate, with most unique virulence-associated genes upregulated at 10 days post inoculation. This expanded arsenal of virulence genes in Che included numerous unique CAZymes, heat shock proteins, and host immune evasion genes, providing a genetic basis for its heightened virulence and thermal tolerance. Among predicted secondary metabolite biosynthetic genes, five genes were shared and two were UIP only in Che. Among the most similar known clusters, putative clavaric acid and choline biosynthesis genes were UIP in both species. Furthermore, four Cps genomic groups indicated potential population-level divergence. This work not only elucidates the potential genetic basis for Che's aggressiveness but also provides candidate genes for future infiltration assays to help identify resistant boxwood germplasm and for developing improved Che-specific rapid diagnostic assays.