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<p>Three native <i>Trichoderma asperellum</i> strains viz., <i>TAIK1, TAIK4,</i> and <i>TAIK5</i> identified through rigorous functional screening of rice rhizosphere isolates and exhibiting strong antagonistic activity against major pathogens viz., <i>Rhizoctonia solani</i>, <i>Ustilaginoidea virens</i>, <i>Xanthomonas oryzae</i>, <i>Sclerotium oryzae</i> along with multiple plant growth–promoting traits, were selected for comprehensive genomic analysis. Comprehensive genome characterization revealed key functional gene families involved in plant defence, secondary metabolite biosynthesis, and growth enhancement. The genomes encoded a diverse set of extracellular lytic enzymes—such as chitinases and β-1,3-glucanases—and antimicrobial peptides, including bacilysin, bacteriocin, and subtilosin, which are essential for pathogen suppression. Genome-wide mining uncovered biosynthetic gene clusters (BGCs) for several secondary metabolites, including enniatin, dimethylcoprogen, clavaric acid, AM-toxin, melanin, aculeacin, anabaenopeptin NZ857, nostamide A, bacitracin, quercetin, surfactin, and lantibiotic. Functional annotation identified genes associated with plant growth promotion, such as those involved in siderophore biosynthesis, Epl1/Sm1, swollenin, ankyrin-repeat, and WD40-repeat domain proteins, contributing to nutrient uptake, root development, and induced systemic resistance. Among the metabolites, 6-pentyl-2H-pyran-2-one (6PP), a volatile compound from TAIK1, demonstrated strong antifungal activity and was selected for further biocontrol application. Phylogenetic analysis of functional genes indicated genetic divergence and specialization among the strains. Furthermore, SSR markers were mined to facilitate population genetics studies and future strain improvement. These findings highlight the potential of TAIK1, TAIK4, and TAIK5 as promising candidates for the development of bioformulations, offering sustainable solutions for rice disease management and supporting novel antibiotic and biofertilizer innovations.</p>

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Genomic cognizance of native strains of antagonistic Trichoderma asperellum from rice fields in India

  • 期刊论文

  • 发表日期：

    2026年7月11日

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  • Sowmya Vanama,
  • Neha Attal,
  • Kalyani M. Barbadikar,
  • Maruthi Pesari,
  • Divya Kattupalli,
  • Raman Meenakshi Sundaram,
  • Kannan Chinnaswami

摘要

Three native Trichoderma asperellum strains viz., TAIK1, TAIK4, and TAIK5 identified through rigorous functional screening of rice rhizosphere isolates and exhibiting strong antagonistic activity against major pathogens viz., Rhizoctonia solani, Ustilaginoidea virens, Xanthomonas oryzae, Sclerotium oryzae along with multiple plant growth–promoting traits, were selected for comprehensive genomic analysis. Comprehensive genome characterization revealed key functional gene families involved in plant defence, secondary metabolite biosynthesis, and growth enhancement. The genomes encoded a diverse set of extracellular lytic enzymes—such as chitinases and β-1,3-glucanases—and antimicrobial peptides, including bacilysin, bacteriocin, and subtilosin, which are essential for pathogen suppression. Genome-wide mining uncovered biosynthetic gene clusters (BGCs) for several secondary metabolites, including enniatin, dimethylcoprogen, clavaric acid, AM-toxin, melanin, aculeacin, anabaenopeptin NZ857, nostamide A, bacitracin, quercetin, surfactin, and lantibiotic. Functional annotation identified genes associated with plant growth promotion, such as those involved in siderophore biosynthesis, Epl1/Sm1, swollenin, ankyrin-repeat, and WD40-repeat domain proteins, contributing to nutrient uptake, root development, and induced systemic resistance. Among the metabolites, 6-pentyl-2H-pyran-2-one (6PP), a volatile compound from TAIK1, demonstrated strong antifungal activity and was selected for further biocontrol application. Phylogenetic analysis of functional genes indicated genetic divergence and specialization among the strains. Furthermore, SSR markers were mined to facilitate population genetics studies and future strain improvement. These findings highlight the potential of TAIK1, TAIK4, and TAIK5 as promising candidates for the development of bioformulations, offering sustainable solutions for rice disease management and supporting novel antibiotic and biofertilizer innovations.