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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 #422097
Research Project: Development of Applied Management Systems for Diseases of Perennial Crops with Emphasis on Vector-Borne Pathogens of Grapevine and Citrus

Location: Crop Diseases, Pests and Genetics Research

Title: Complete mitochondrial genomes of biological control stains in the Trichoderma harzianum Rifai complex (strains DL1-3, KC1-3, and PAR10) isolated from Californian grapevines

Author
item Wallis, Christopher
item Chen, Jianchi

Submitted to: Mitochondrial DNA Part B
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/22/2025
Publication Date: 9/2/2025
Citation: Wallis, C.M., Chen, J. 2025. Complete mitochondrial genomes of biological control stains in the Trichoderma harzianum Rifai complex (strains DL1-3, KC1-3, and PAR10) isolated from Californian grapevines. Mitochondrial DNA Part B. 10(10). https://doi.org/10.1080/23802359.2025.2552822.
DOI: https://doi.org/10.1080/23802359.2025.2552822

Interpretive Summary: Species identification for the genus Trichoderma is very challenging despite it containing many important industrial and biological control agent strains. Thus, the mitochondrial genomes were obtained for three biological control strains, DL1-3, KC1-1, and PAR10, to assist in species identification. Phylogenetic trees using mitochondrial genomes were compared with trees using housekeeping genes. Comparisons of mitochondrial genomes appeared far better at resolving species than those made with housekeeping genes. Therefore, the obtained mitochondrial genome resources for DL1-3, KC1-1, and PAR10 will assist in future efforts to properly identify Trichoderma strains to species.

Technical Abstract: The genus Trichoderma contains a variety of useful fungi that can be used as biological control agents among other purposes, but classification remains challenging. Mitochondrial genome sequence analyses may provide a tool for species identification. Thus, the complete mitochondrial genomes of Trichoderma Rifai strains DL1-3, KC1-1, and PAR10 were obtained. The mitochondrial genome size of strain DL1-3 is 29,197 bp, the size of strain KC1-1 is 27,631 bp, and the size of stain PAR10 is 29,122 bp. All strains contained a 25 or 26 tRNA genes, 2 rRNA genes, and 15 core mitochondrial protein coding genes. PAR10 also had an additional coding sequence for a putative protein. Phylogenetic analysis of available mitochondrial sequences suggested that T. harzianum may exist as a species complex, with DL1-3 linked closely to Trichoderma simmonsii, KC1-1 linked to T. harzianum, and PAR10 linked to T. afroharzianum. Phylogenetic trees made with housekeeping genes ITS, RPB2, and TEF1 differed on the placement of KC1-1 and PAR10, but did confirm DL1-3 was consistent with T. simmonsii. This suggest the identities of the Trichoderma harzianum complex remains in flux, but comparisons of the complete mitochondria genomes provided valuable information in resolving questions of species identification.