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ARS Home » Pacific West Area » Parlier, California » San Joaquin Valley Agricultural Sciences Center » Crop Diseases, Pests and Genetics Research » Research » Publications at this Location » Publication #430641
Research Project: Identifying Vulnerabilities in Vector-host-pathogen Interactions of Grapevine and Citrus Pathosystems to Advance Sustainable Management Strategies

Location: Crop Diseases, Pests and Genetics Research

Title: Utilizing mitochondrial genome sequences to understand population diversity among Trichoderma species

Author
item Wallis, Christopher
item Chen, Jianchi
item Mekdara, Nalong

Submitted to: Frontiers in Fungal Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/22/2026
Publication Date: 5/15/2026
Citation: Wallis, C.M., Chen, J., Mekdara, N. 2026. Utilizing mitochondrial genome sequences to understand population diversity among Trichoderma species. Frontiers in Fungal Biology. 7. Article 1810157. https://doi.org/10.3389/ffunb.2026.1810157.
DOI: https://doi.org/10.3389/ffunb.2026.1810157

Interpretive Summary: Trichoderma is a fungal genus that contains strains useful for many commercial and industrial purposes including biofuel production, bioremediation of contaminated sites, and biological control agents that combat plant disease. However, the diversity of Trichoderma species and strains is underappreciated, and improved approaches to characterize newly collected isolate are needed. Thus, mitochondrial genome sequences were obtained from new Trichoderma isolates from Californian vineyards. These were then used with previously published Trichoderma mitochondrial genomes to obtain a phylogenetic tree to infer the placement of these strains to clades and species. The phylogenetic tree using the mitochondrial genome was compared with those using available annotated nuclear genomes and was found to be consistent in placement of strains and species to clades. Thus, mitochondrial genomes, which are easier to assemble than annotated nuclear genomes, may be used to identify promising strains more rapidly.

Technical Abstract: Biopesticides, including those containing various Trichoderma species, may provide improved control of fungal diseases of woody perennials including grapevines. Thus, Trichoderma isolates were obtained from grapevines in California, U.S.A., with eight strains demonstrated to provide biological control against fungal pathogens. These were determined via phylogenetic analyses to be one of six different species: Trichoderma asperellum, Trichoderma capillare, Trichoderma harzianum, Trichoderma saturnisporopsis, and two novel Trichoderma species (Trichoderma sp. DL1-3 and Trichoderma sp. PAR10). However, little is known about strain genetic diversity. Therefore, efforts were undertaken to characterize and compare obtained mitochondrial genomes with those previously published from related Trichoderma species. For this effort, the mitochondrial genomes of T. asperellum strain TLI, T. capillare strains KC2-2 and SLO1-1, and T. saturnisporopsis strain RSI were obtained, annotated and compared to the other Californian strains and 23 other Trichoderma species genomes. All analyzed species had the same major protein coding genes, rRNA regions, and tRNA coding sequences. Further, specific introns were observed to be associated with distinct clades within the Trichoderma genus, and these could be used to develop markers to quickly assign an unknown Trichoderma into a specific clade. Knowledge of Trichoderma mitochondrial genomes should improve understanding about this fungal genus.