Browsing by Author "Korkmaz E.M."

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    Trichoderma atroviride suppresses Fusarium graminearum by altering primary and secondary metabolite biosynthesis profiling
    (John Wiley and Sons Inc, 2023) Özkale E.; Yörük E.; Budak M.; Korkmaz E.M.
    The use of Trichoderma spp. offers an ecologically friendly tool for the struggle with mycotoxigenic Fusarium spp. Here, the alterations in transcriptome level were investigated in 6-day-old Fusarium graminearum cultures treated with Trichoderma atroviride and nontreated with T. atroviride (FGc), using whole transcriptome sequencing to better understand the associated biological processes. Transcriptome analysis indicated a total of 55 up-regulated genes and 728 down-regulated genes with padj < 0.05. Enrichment analysis revealed that the up-regulated genes were related to fatty acid biosynthesis, AMP-dependent biosynthesis, amino acid recognition/activation processes and secondary metabolite production, whereas down-regulated genes were involved in amino acid synthesis, oxidation–reduction processes, metal ion-binding and metabolic/catalytic activities. Among the down-regulated genes, the expression of pigmentation-related genes such as aurO, gip1 and aurR2 was remarkable. Similarly, the expression levels of key enzyme-coding genes involved in deoxynivalenol mycotoxin production were significantly decreased in the range of −1.77 and −2.94. For up-regulated genes, nonribosomal peptide synthetase and polyketide synthase genes were notably distinguished from the remaining down-regulated genes as these genes can be involved in biosynthesis of common secondary metabolites. The results clearly emphasize that T. atroviride repressed the biosynthesis of primary metabolites in F. graminearum while simultaneously up-regulating the expression of genes involved in the synthesis of secondary metabolites. This is the first report showing how T. atroviride leads to transcriptome alterations and the findings suggest that T. atroviride could serve as an effective fungus by employing a wide variety of strategies against phytopathogenic fungi. © 2023 The Authors. Plant Pathology published by John Wiley & Sons Ltd on behalf of British Society for Plant Pathology.
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    Mitogenome evolution in Trichoderma afroharzianum strains: for a better understanding of distinguishing genus
    (Canadian Science Publishing, 2024) Özkale E.; Doğan Ö.; Budak M.; Korkmaz E.M.
    Trichoderma afroharzianum (Hypocreales) is known as an important mycoparasite and biocontrol fungus and feeds on fungal material by parasitizing other fungi. Recent studies indicate that this species is also an ear rot pathogen in Europe. Here, the complete mitochondrial genome of three T. afroharzianum strains was sequenced using next-generation sequencing and comparatively characterized by the reported Trichoderma mitogenomes. T. afroharzianum mitogenomes were varying between 29 511 bp and 29 517 bp in length, with an average A + T content of 72.32%. These mitogenomes contain 14 core protein coding genes (PCGs), 22 tRNAs, two rRNAs, one gene encoding the ribosomal protein S3, and three or four genes including conserved domains for the homing endonucleases (HEGs; GIY-YIG type and LAGLIDADG type). All PCGs are initiated by ATG codons, except for atp8, and all are terminated with TAA. A significant correlation was observed between nucleotide composition and codon preference. Four introns belonging to the group I intron class were predicted, accounting for about 14.54% of the size of the mitogenomes. Phylogenetic analyses confirmed the positions of T. afroharzianum strains within the genus of Trichoderma and supported a sister group relationship between T. afroharzianum and T. simmonsii. The recovered trees also supported the monophyly of all included families and of the genus of Acremonium. The characterization of mitochondrial genome of T. afroharzianum contributes to the understanding of phylogeny and evolution of Hypocreales. © 2024 The Author(s).