Phylogenomic analysis with related Sordariomycetes supports a monophyletic origin and clear genetic separation of Trichoderma. The genus arose 100\u201366\u2009Ma (million years ago) during the Late Cretaceous, coinciding with angiosperm rainforest expansion14<\/a>. The last common ancestor likely diverged around the K\u2013Pg boundary during global crises of volcanism, impact, cooling and mass extinction15<\/a>. Warm intervals (Pliocene, Eocene) did not trigger diversification, but the cooler, drier Oligocene (34\u201323\u2009Ma) coincided with the emergence of the extant Harzianum, Longibrachiatum and Viride clades and a few lone lineages (Fig. 1<\/a>). Later Miocene aridification and rainforest loss are mirrored by pronounced phylogenetic branching, suggesting diversification under adverse climatic pressures.<\/p>\n Fig. 1: Phylogenomic analysis of Trichoderma within Sordariomycetes. Time-calibrated phylogeny inferred from 436 single-copy orthogroups showing the evolutionary history of Trichoderma within Sordariomycetes. Node labels indicate mean divergence times (Ma); solid dots denote 100% bootstrap support, and horizontal bars indicate 95% highest posterior density intervals. Trichoderma taxonomy is simplified for clarity; detailed molecular identifications and taxonomic notes are provided in Supplementary Table 1<\/a>. Icons summarize major ecological roles and reproductive modes. Genome-size bars show protein-coding gene (PCG) counts normalized to T. atroviride (Supplementary Table 3<\/a>). Pie charts summarize taxon-specific HOG composition (PFAM-annotated genes, SSPs and genes of unknown function); numbers above pies indicate the number of taxon-specific HOGs, and percentages below indicate the fraction of co-evolving genes. The inset (upper left) shows general average temperature (GAT, \u00b0C) across geological epochs15<\/a>, with the Cretaceous\u2013Paleogene (K\u2013Pg) boundary and the warm, humid period that favoured tropical rainforests (relevant for Trichoderma evolution) highlighted. Time periods are abbreviated as follows: N, Neogene; Q, Quaternary.<\/p>\n Source data<\/a><\/p>\n Although the Longibrachiatum clade has relatively smaller genomes6<\/a>,7<\/a>, Trichoderma overall maintains a consistent genome size distinct from other Hypocreales, with ~8,000\u201313,700 protein-coding genes (Supplementary Table 3<\/a>). Most genomic metrics matched other hypocrealean fungi and our earlier studies7<\/a>. Expansins numbered 5\u201310\u2014twice those in reference genomes and only matched by Fusarium\u2014highlighting adaptation to moisture and plant-associated niches16<\/a>.<\/p>\n Trichoderma harbours 1,123 genus-exclusive hierarchical orthologous groups (HOGs), comprising 16.7% of its core genome (6,689 genes), versus only 62 (<1%) in Metarhizium (Fig. 1<\/a>). This marked distinction underscores the unique genetic identity of Trichoderma, at least compared with the hypocrealean genomic data available to date. Across clades, over half of clade-specific genes encode small secreted proteins (SSPs) of unknown function; protein family (PFAM) domains were found in only 3\u201313% of HOGs compared with 50% in other Sordariomycetes. The proportion of intracellular proteins of unknown function was consistent across groups (Fig. 1<\/a>).<\/p>\n Gene co-evolution analysis showed that ~1% of Trichoderma core genes share an evolutionary trajectory, with higher proportions in individual clades\u20144.78% in Longibrachiatum and 10.12% in Viride (Fig. 1<\/a> pie charts). These values were unaffected by sample size or ancestral node age, suggesting radiation and ecological specialization, especially compared with Metarhizium, where 30% of core genes co-evolve (Fig. 1<\/a> pie charts).<\/p>\n Thus, phylogenomics confirms that Trichoderma formed as a genetically compact genus in the humid and warm Late Cretaceous, with its genetic coherence reflected in uniform morphological traits, such as verticillate conidiophores with green spores and characteristic structures of sexual reproduction2<\/a>. Yet from the cooler Oligocene onward, diversification produced marked genetic variation without corresponding morphological or macroecological shifts (Fig. 1<\/a>).<\/p>\n Spore germination of Trichoderma may be enhanced in phyllosphere microbial mats<\/p>\n Because conditions that trigger conidial germination largely determine where Trichoderma can initiate its life cycle, we assessed spore germination across 95 carbon sources using BIOLOG FF microplates. l-Phenylalanine substantially improved early development in most Trichoderma strains, with glycogen also effectively enhancing germination. Other compounds such as adenosine, d-arabitol, i-erythritol and l-alanine supported germination to varying degrees, indicating strain-specific responses (Extended Data Fig. 1<\/a>). Species used in agronomy like T. atroviride and Trichoderma guizhouense preferred glycogen and showed no response to l-phenylalanine, suggesting adaptations to nutrient-rich environments. Most strains, particularly T. atroviride, T. guizhouense and T. harzianum, germinated as effectively in pure water as in many carbon sources tested, reflecting adaptations to oligotrophic and moist habitats. Such carbon sources as fumaric acid, succinic acid and n-acetyl sugars were unfavourable for life-cycle initiation. This evaluation also revealed species-specific ecological adaptations: slower development in T. harzianum suggests parsimonious resource utilization beneficial in low-nutrient conditions, whereas Trichoderma velutinum Triveli and Trichoderma zeloharzianum showed rapid germination, indicating a competitive advantage on quickly colonizable substrates (Extended Data Fig. 1<\/a>).<\/p>\n The genus-wide ability to germinate in water, together with stimulation by l-phenylalanine, glycogen and related compounds, suggests that Trichoderma life-cycle initiation may be particularly enhanced in niches where amino acids, storage polysaccharides and sugar alcohols are locally enriched. Such conditions occur, for example, in phyllosphere microbial mats and other plant-associated microhabitats, where these compounds are reported as common microbial osmoprotectants17<\/a>.<\/p>\n Nutritional preferences suggest mycoparasitism in arboreal biofilms<\/p>\n The next vegetative stage, characterized by exponential growth, revealed consistently broad nutritional versatility across Trichoderma when tested on 95 carbon sources (Extended Data Figs. 2<\/a> and 3<\/a>). Variability between clades was minor, but related species and strains showed marked differences, indicating diverse idioadaptations (fine-scale, lineage-specific ecological adjustments). Overall for the genus, at least 41 substrates and water supported growth, 36 were suboptimal, and 18 yielded biomass no greater than the water control.<\/p>\n The optimal substrate for all Trichoderma strains was N-acetyl-d-glucosamine, the chitin monomer of fungal cell walls and arthropod exoskeletons, underscoring its mycoparasitic capacity, competitive role in fungal communities and occasional insect parasitism2<\/a>. Sugar alcohols such as glycerol, d-sorbitol, i-erythritol, d-arabitol and d-mannitol also promoted robust growth, reflecting adaptation to osmoprotectants abundant in arboreal microbial mats (phylo-\/xylosphere)17<\/a>. These complex polysaccharide- and stress-protectant-rich habitats contrast with the simpler, root-exudate-driven systems of rhizosphere and bulk soil18<\/a>.<\/p>\n Sugars from plant biomass decomposition\u2014such as maltotriose, cellobiose, trehalose, glucose, fructose, mannose, ribose, galactose, melibiose and xylose\u2014also supported robust but strain-specific growth, suggesting effective utilization in soil and rhizosphere environments where complex organic matter is abundant (Extended Data Fig. 2<\/a>, and Supplementary Data 1<\/a> and 2<\/a>).<\/p>\n Moderate growth on substrates such as other osmoprotectants (raffinose, lactulose), phenolics (arbutin), sugar alcohols (xylitol), unusual metabolites (\u029f-phenylalanine, \u029f-fucose) and polysaccharides (glycogen, dextrin) suggests broad ecological adaptability, although these rarely supported peak growth and may act as secondary energy sources or germination triggers (vide supra). By contrast, limited growth on specialized substrates\u2014particularly organic acids (fumaric, succinic) and amino acids (l-glutamic, l-asparagine)\u2014indicates metabolic stress and points to environments (for example, acidic, fermentative) unfavourable for Trichoderma colonization (Extended Data Fig. 2<\/a>).<\/p>\n Similar to spore germination, growth preferences showed no strict concordance with phylogeny, implying adaptive convergence. Extended Data Fig. 3<\/a> illustrates highly strain-specific \u2018nutritional barcodes\u2019. Three Harzianum clade strains (T. zeloharzianum, Trichoderma lixii, Trichoderma breve), recently isolated from tropical leaves, grew exceptionally fast on d-sorbitol and other sugar alcohols, suggesting phyllosphere adaptation. Several Harzianum strains also used N-acetyl-d-mannosamine, a sialic-acid precursor typical of animal tissues and some prokaryotes19<\/a>, pointing to possible links with insect gut microbiomes or vertebrate mucosa. In addition, selected Viride clade strains related to T. atroviride metabolized sucrose and maltose, implying potential for endophytic development (Extended Data Fig. 2<\/a>).<\/p>\n In summary, the nutritional profile of Trichoderma aligns with its common roles as mycoparasite and saprotroph on microbially colonized wood, as endo- and epiphyte, and in the rhizosphere. It also suggests involvement in microbial interactions within arboreal and rhizospheric biofilms and confirms that these fungi can exploit plant biomass.<\/p>\n Genotype and nutrition shape reproductive strategies in Trichoderma<\/p>\n To further assess fitness-related traits of Trichoderma, we quantified asexual reproduction using REPAINT (Reproduction Potential Artificial Intelligence20<\/a>), which analyses time series images from BIOLOG microplates to extract numerical data on hyphal growth and conidial coverage.<\/p>\n N-Acetyl-d-glucosamine, sugar alcohols and simple sugars generally supported extensive aerial mycelium and abundant conidiation (Supplementary Data 3<\/a>). By contrast, m-inositol, glycogen and dextrin promoted conidiation with little aerial mycelium. Certain amino acids induced aerial hyphae without conidiation in nearly all strains, suggesting either exploratory growth under metabolic stress or initiation of sexual reproduction. Many suboptimal carbon sources supported vegetative growth without conidiation.<\/p>\n We identified four distinct reproductive strategies with marked interspecific variability, suggesting underlying speciation processes (Fig. 2<\/a>). T. asperellum consistently produced abundant conidia with little aerial mycelium, indicative of a copiotrophic, r-selected strategy favouring rapid reproduction in resource-rich environments; this pattern also characterized the mushroom pathogens Trichoderma pleuroticola and Trichoderma amazonicum and the endophyte Trichoderma endophyticum. By contrast, T. reesei and Trichoderma minutisporum, typically known in nature from sexual stages (Fig. 1<\/a>), formed dense aerial mats with few conidia, reflecting a K-selected strategy emphasizing competitive ability and resource efficiency. Similar behaviour occurred in phylogenetically unrelated species such as Trichoderma spirale and Trichoderma brevicompactum. A third strategy\u2014rapid vegetative growth with moderate conidiation\u2014was characteristic of agronomically used species like T. atroviride and T. guizhouense, possibly compatible with adaptations to endophytic development. Finally, T. harzianum, T. afroharzianum and T. virens showed high reproductive plasticity, producing both dense aerial mycelium and conidia across diverse substrates, exemplifying ecological opportunism.<\/p>\n Fig. 2: Developmental strategies of Trichoderma analysed using the REPAINT assay. a, Sample diagrams show the relationship between linear growth rate (bubble size, measured as optical density (OD750) per 24\u2009h; strain- and carbon-specific values are listed in Supplementary Data 1<\/a>\u20133<\/a>) on 95 carbon sources and water, and the corresponding development of aerial hyphae after 96\u2009h (x axis) and conidiation after 120\u2009h (y axis), expressed as percentage of well surface coverage. b, Principal component analysis of developmental profiles of 37 Trichoderma strains based on the complete REPAINT and BIOLOG dataset (Supplementary Data 1<\/a>). Axes indicate PC1 (41.5% variance) and PC2 (32.5% variance). Bubble size represents the mean growth rate across all carbon sources, used here as a synthetic summary measure. c, Schematic diagram of the Trichoderma life cycle, illustrating asexual reproduction and the formation of aerial mycelium putatively associated with sexual development. Colours correspond to four putative reproductive strategies, consistent across panels: green, asexual\/clonal r-strategy (abundant conidia, minimal aerial hyphae); yellow, putative sexual K-strategy (dense aerial mats, few conidia); blue, putative endophytic strategy (rapid vegetative growth, moderate conidiation); purple, holomorphic\/opportunistic strategy (plastic responses across substrates).<\/p>\n Source data<\/a><\/p>\n Variation was especially pronounced among close relatives, notably between T. velutinum strains and the formerly cryptic sympatric species T. asperellum and T. asperelloides21<\/a> (Extended Data Fig. 4<\/a>), pointing to divergent speciation within these clades. Such sharp differences in reproductive strategy among closely related and co-occurring taxa are suggestive of character displacement (vide infra) and idioadaptive processes likely driving speciation in Trichoderma.<\/p>\n Trichoderma species vary in spore dispersal and stress tolerance<\/p>\n We quantified pluviophilous (rain-mediated) and anemophilous (wind-mediated) spore dispersal, along with survivability under temperature extremes and desiccation (Fig. 3<\/a> and Supplementary Fig. 1<\/a>). About one-third of strains were anemophilous, another third pluviophilous, and the remainder produced conidia not aligned with these mechanisms, likely dispersed through other media, for example, zoochory.<\/p>\n Fig. 3: Relative fitness of Trichoderma strains. Relative fitness of strains normalized to T. atroviride, which is used as the reference taxon of the genus (shown as a circle). Growth rates on differentiating carbon sources (for example, N-acetyl-d-mannosamine, glycogen) are shown together with developmental strategy, spore stress tolerance and dispersal efficiency. The last column (\u2018Product\u2019) represents the multiplicative composite of the three fitness-related traits (development, stress tolerance and dispersal). Stars mark strains whose spores did not survive cold or drought conditions tested in this study, resulting in a product value of 0. Values are displayed on a logarithmic scale, highlighting the drastic differences in performance across strains. Strains are ordered according to the phylogeny in Fig. 1<\/a>.<\/p>\n Source data<\/a><\/p>\n Trichoderma spores were more vulnerable to desiccation than to temperature extremes, with many strains failing to survive (Fig. 3<\/a>). Air-dispersed conidia resisted extreme temperatures, whereas water-dispersed ones were highly susceptible to desiccation (Supplementary Fig. 1<\/a>). Cold-resistant spores also tolerated heat, but desiccation tolerance was uncoupled from thermal resistance, indicating distinct adaptive mechanisms.<\/p>\n Spores of T. afroharzianum, widely used in agriculture and recently reported as a maize pathogen10<\/a>, showed strong stress resistance and anemophilous dispersal. By contrast, T. asperellum, despite prolific conidiation (vide supra), dispersed poorly by air or water, suggesting reliance on alternative strategies. These contrasting profiles illustrate adaptive radiation within the genus and its occupation of diverse ecological niches.<\/p>\n Fitness mapping reveals phenotypic divergence in Trichoderma<\/p>\n We quantified fitness-related parameters across the Trichoderma life cycle, including growth rates on various carbon sources, reproductive potential, spore dispersal and stress resilience. These data were integrated into a relative fitness map, showing growth on universally optimal N-acetyl-d-glucosamine and differentiating substrates such as N-acetyl-d-mannosamine, saccharides and glycogen (Fig. 3<\/a>). Metrics, combined with averaged REPAINT profiles and spore properties, were normalized to T. atroviride\u2014closely related to the type species Trichoderma viride5<\/a>\u2014and plotted against the phylogenomic tree as in Fig. 1<\/a>. Whereas Fig. 3<\/a> highlights variability in fitness traits, Extended Data Fig. 5<\/a> shows that genome inventories (proteins, transcription factors, transporters, enzymes, biosynthetic clusters) remain relatively compact. This asymmetry suggests that phenotypic differences among strains are greater than variation in genome content (Supplementary Table 3<\/a>).<\/p>\n The relative fitness map revealed substantial ecophysiological diversity, with greater differences among closely related species than between clades and similarities between unrelated strains, consistent with processes such as character displacement22<\/a> speciation and convergent adaptation within the genus (Fig. 3<\/a>). Sympatric strain groups (for example, Tri5505\u2013Tri5757, Trisp\u2013Trien in Harzianum; Tristr and Triev in Viride) showed marked disparities in fitness despite co-isolation. Strains of T. amazonicum (Triam, Tripleu), which diverged ~0.4\u2009Ma (Fig. 1<\/a>), also contrasted strongly, with Triam outperforming Tripleu in this set-up. At deeper scales, contrasts appeared between Trivel and Triveli (T. velutinum) and between T. asperellum and T. asperelloides (~4\u20136\u2009Ma divergence), the latter known to co-occur in nature21<\/a>. Similarly, T. guizhouense (Trigui) and T. harzianum (Triha) strains, although not sympatric in this dataset, are reported to co-occur20<\/a> at the species level. These examples highlight multiple instances where closely related taxa diverge in trait profiles, reflecting evolutionary dynamic consistent with possible character displacement.<\/p>\n In this approach, T. atroviride\u2014widely marketed for mycoparasitism, plant immune induction and stress resilience1<\/a>,2<\/a>\u2014was outperformed by T. afroharzianum and T. guizhouense, both showing greater conidial survivability (Fig. 3<\/a>). Conversely, T. asperellum, despite prolific conidiation, showed poor dispersal and strong temperature sensitivity, consistent with adaptation to stable habitats. Such variability in fitness traits (Fig. 3<\/a>) contrasted with the compact distribution of genome features (Extended Data Fig. 5<\/a>), underscoring that no single strain dominates across metrics; each performs best in conditions matching its ecological niche.<\/p>\n Distinctive ecophysiological traits and biosecurity relevance of Trichoderma<\/p>\n To further probe ecophysiology of Trichoderma, we assessed multiple qualitative traits, finding universally strong proteolysis, robust mycoparasitism and negligible antibacterial activity (Supplementary Data 4<\/a>). Despite frequent rhizosphere applications1<\/a>, all species grew poorly in bulk soil (three soil types, sterile and non-sterile), with only T. virens and T. asperellum developing in soil if sterilized. Nevertheless, all strains promoted plant growth (Supplementary Fig. 2<\/a>), indicating rhizosphere competence independent of bulk-soil growth. In general, Trichoderma also showed a clear preference for protein-rich substrates (fungal biomass, soybeans) over nitrogen-poor cellulosic materials (for example, rice straw, magnolia leaves) (Supplementary Data 4<\/a>).<\/p>\n Light generally enhanced spore production, although without genus-wide circadian rhythms; some strains also conidiated in darkness (Supplementary Data 4<\/a>). Conidial rings and conidiation-associated guttation occurred across clades but often contrasted sharply between close relatives (for example, two T. velutinum strains), suggestive of character displacement. Most strains thrived under oligotrophic conditions and showed sensitivity to mechanical injury, which variably influenced conidiation.<\/p>\n Enzyme activities such as amylase, cellulase and lipase were common but highly variable among strains, with no correlation to each other or to phylogeny (Supplementary Data 4<\/a>). By contrast, cutinase activity on polycaprolactone (PCL) was characteristic of the Harzianum clade, whereas Viride strains excelled in siderophore-mediated iron sequestration (Supplementary Data 4<\/a>).<\/p>\n Species varied in their ability to form buoyant colonies and produce conidia while floating, underscoring the importance of this trait in Trichoderma biology (Supplementary Data 4<\/a>). Overall, the genus shows distinctive traits with frequent divergence among relatives including those of sympatric origin (for example, suggestive of character displacement) and convergence among unrelated taxa, while few adaptations align consistently with phylogeny.<\/p>\n Because agronomic use entails intentional mass release4<\/a>, the observed phenotypic diversity has direct bearing on biosecurity. We therefore contextualize some of these readouts in a first-tier biosecurity framework for agronomically relevant strains that integrates taxonomy, fitness profiling and pathogenicity records in humans and plants (Fig. 4<\/a>).<\/p>\n Fig. 4: Framework for evaluating Trichoderma biosecurity for agronomic applications. a, Conceptual flowchart for biosecurity evaluation. Candidate isolates agronomically relevant for crop-beneficial applications undergo taxonomic identification5<\/a>, fitness profiling and a species-level biosecurity assessment against authoritative sources (EPPO, Centre for Agriculture and Bioscience International (CABI), National Plant Protection Organization (NPPO)) alerts, leading to classification into categories of biosecurity concern to prioritize strains for further evaluation. b, Field example of Trichoderma-associated premature sprouting of maize ears, Shandong, China (October 2025). c, Species-level evidence. Blue flag symbols denote literature reports for clinical occurrence8<\/a> and for plant pathogenicity in T. lixii11<\/a>, T. afroharzianum10<\/a>, T. virens12<\/a> and T. longibrachiatum13<\/a>. Species in bold are those with documented plant and human pathogenicity. Pathogenicity in mushrooms is not mapped here, because although the number of reported species is relatively limited9<\/a>, mycoparasitism is an innate trait of the genus28<\/a>, making it reasonable to assume that all strains carry potential risk for mushroom growers. Similarly, the production of mycotoxins\u2014such as gliotoxin in T. virens31<\/a>, phytotoxins including harzianic acid in the Harzianum species complex58<\/a>, sorbicillins in section Longibrachiatum59<\/a> and trichothecenes in T. brevicompactum60<\/a>\u2014is not indicated here, as a comprehensive genus-wide survey of secondary metabolites has not yet been performed. d, Examples of biosecurity-relevant phenotypes assessed in this study. Yellow flags summarize traits relevant to environmental persistence and spread: dispersal (air), stress tolerance and high fitness (fast growth, abundant conidiation, versatile nutrition). These properties and species-level reports serve as screening cues, not hazard designations; their presence highlights strains that warrant additional, context-specific risk evaluation before deployment.<\/p>\n Regulatory genes and SSPs underpin ecological adaptation in Trichoderma<\/p>\n We demonstrated that Trichoderma spp. maintain genomic cohesion while undergoing adaptive radiation and developing considerable ecophysiological variability that often leads to phenotypic convergence among genetically distinct taxa, including several species important in agriculture. Using Support Vector Machine (SVM) analysis with Python scikit-learn v0.17, we evaluated each strain genome against more than 140 phenotypic parameters, among which 72 showed statistical significance. These parameters were catalogued in a binary matrix, highlighting the presence, absence or uncertainty (in cases of heterogeneous or intermediate responses across strains) of each trait (Supplementary Data 1<\/a>). Our approach identified phenotype-associated orthogroups (PAOGs) that were statistically significantly correlated with distinct phenotypic traits, facilitating predictions in cases with ambiguous phenotypic profiles. Unlike phenologues, which are cross-species phenotype\u2013phenotype relationships inferred from shared orthologous gene sets23<\/a>, the PAOG framework identifies genotype\u2013phenotype associations within a clade of closely related species.<\/p>\n Statistical analysis revealed substantial gene segregation across quantitative 45 growth profiles on specific carbon sources and 27 qualitative or summative phenotypes. Among others, these included traits such as mycoparasitic vigour and mechanical injury responses ranging from stimulation to non-response (Fig.\u20095<\/a> and Supplementary Table 4<\/a>). For example, phenotypes such as the degradation of PCL correlated with the enhanced presence of certain oxidoreductase enzymes (PF00106), aldolases (PF03328), protective proteins (PF04479, PF07976, PF01494) and SSPs of unknown function, which collectively may enhance polymer breakdown and mitigate potential toxic effects. Conversely, subtilases (PF00082), NWD (NACHT\u2013WD repeat) NACHT-NTPase-related domains (nucleotide-binding oligomerization domain proteins) (PF17100) and several intracellular proteins potentially weaken the response to mechanical injury by reducing cellular damage.<\/p>\n Fig. 5: Phenotype\u2013genotype association in Trichoderma. a, SVM analysis: results for 37 Trichoderma strains using SVM to correlate binary phenotypic traits with genomic data. Selected traits include growth rate on d-xylose, response to mechanical injury (see b), ability to degrade PCL and putative clonality (inversely related to putative sexuality). Each phenotype is paired with the distribution of statistically significant associated HOGs, observed and predicted phenotypes and probability segregation plots\u2014probability of phenotype absence (0) on the x axis and presence (1) on the y axis. Strains are horizontally ordered as in Fig. 1<\/a>. SSPs without known functions are denoted. The comprehensive phenotypic profile is provided in Supplementary Data 1<\/a>\u20134<\/a>. b, Diversity of mechanical injury responses in Trichoderma illustrates varied responses to mechanical injury induced by a cold, sterile scalpel 72\u2009h before observation, with arrows highlighting resulting scars: yellow arrow, the stimulation of conidiation; black arrow, inhibition; white arrow, no response. The complete phenotypic profile of these responses is available in Supplementary Data 4<\/a>.<\/p>\n Source data<\/a><\/p>\n The comprehensive analysis of PAOGs across 72 phenotypes identified 775 occurrences of 600 unique HOGs, with the majority transcribed and attributed to shell genomes (the portion of a genome that is neither unique to a particular strain (strain-specific) nor common to all species within a genus (core genome)) (Supplementary Table 4<\/a> and Supplementary Data 1<\/a>). Among these, 145 occurrences (20%) are intracellular proteins of unknown function (Fig. 6a<\/a>). The second most numerous group comprised SSPs, emphasizing their role in fitness-related adaptations. Enzymes and transporter proteins showed more association with nutrition-related phenotypes, while genes involved in stress mitigation were detected in association with all kinds of phenotypes.<\/p>\n Fig. 6: Trichoderma phenotype-associated genes detected in this study. a, Annotation of 600 unique PAOGs associated with 72 phenotypes where statistically significant segregation was observed. Numbers indicate occurrences (total 775) within the dataset (Supplementary Table 4<\/a> and Supplementary Data 1<\/a>). b, Composition of transcription factor families among PAOGs compared with their distribution in the full Trichoderma genomes. Asterisks (*) indicate transcription factor families detected among PAOGs but not recovered from the remainder of the genome in this comparative analysis (that is, present only in the PAOG subset). c, Comparative counts of PAOGs, secondary metabolite clusters, glycoside hydrolases, transcription factors and total proteins across Trichoderma clades, normalized to the 369 HOGs in T. atroviride. The Longibrachiatum clade shows a marked reduction in PAOGs and secondary metabolite clusters, while glycoside hydrolases (are only slightly reduced in proportion to the smaller total protein count. GH, glycoside hydrolase; PKS, polyketide synthase; TF, transcription factor; P450, cytochrome P450 monooxygenases; MFS, major facilitator superfamily transporters; SDH, short-chain dehydrogenase\/reductase; FAD, flavin adenine dinucleotide (FAD-binding proteins\/domains); Hyd, hydrolases (\u03b1\/\u03b2-hydrolase fold proteins); Pept, peptidases\/proteases; AAA, ATPases associated with diverse cellular activities; NACHT, NACHT NTPase domain (nucleotide-binding oligomerization domain); ABC Tran, ATP-binding cassette transporters; MCP, mitochondrial carrier proteins; DUF, domain of unknown function; FSTF, fungal-specific transcription factor domain; ZF, zinc finger; bZIP, basic leucine zipper transcription factors.<\/p>\n Source data<\/a><\/p>\n The most profound group of PAOGs with known functionality encoded such regulatory proteins as DNA-binding transcription factors and \u2018fungal-specific transcription factors\u2019 (PF11951, PF04082) that do not bind DNA but are involved in transcriptional regulation in fungi24<\/a>. Transcription factors, especially zinc clusters (PF00172), dominated the regulatory PAOGs, with a significantly higher prevalence compared to the whole genome, suggesting a focused functional role in regulatory processes. However, homeodomain and CCCH-type Zn-finger (ZnF) families, although common in genomes, were absent from PAOGs, indicating selective regulatory deployment (Fig. 6b<\/a>). This trend points to a bias towards Zn clusters over other major families such as C2H2 ZnF, which are underrepresented in PAOGs. Further phylogenetic analysis revealed clade-specific usage of transcription factors, underscoring the complex regulatory landscape that facilitates adaptation of Trichoderma to diverse environmental conditions (Extended Data Fig. 6<\/a>). Genes encoding ankyrin repeats (PF12796 and PF00023) were also frequently detected among PAOGs being mainly associated with nutrition (Supplementary Table 4<\/a>).<\/p>\n![\"figure](\"https:\/\/www.newsbeep.com\/ie\/wp-content\/uploads\/2026\/03\/41564_2026_2260_Fig1_HTML.png\")
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