REFERENCES
Abascal, F., Zardoya, R., & Posada, D. (2005). ProtTest: selection of best-fit models of protein evolution. Bioinformatics , 21 : 2104–2105.
Abe, I., Naito, K., Takagi, Y, & Noguchi, H. (2001). Molecular cloning, expression, and site-directed mutations of oxidosqualene cyclase from Cephalosporium caerulens. Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression , 1522 : 67–73.
Adelin, E., Servy, C., Martin, M.T., Arcile, G., Iorga, B.I., Retailleau, P. … Ouazzani, J. (2014). Bicyclic and tetracyclic diterpenes from a Trichoderma symbiont of Taxus baccata. Phytochemistry , 97 : 55–61.
Bansal, R., & Mukherjee, P. K. (2016). The terpenoid biosynthesis toolkit of Trichoderma. Natural Product Communications , 11 : 1934578X1601100.
Baroncelli, R., Piaggeschi, G., Fiorini, L., Bertolini, E., Zapparata, A., Pè, M.E., … Vannacci, G. (2015). Draft Whole-Genome Sequence of the biocontrol agent Trichoderma harzianum T6776. Genome Announcements , 3 : e00647-15.
Baroncelli, R., Zapparata, A., Piaggeschi, G., Sarrocco, S., & Vannacci, G. (2016). Draft Whole-genome sequence of Trichoderma gamsii T6085 , a promising biocontrol agent of Fusarium Head Blight on wheat. Genome Announcements , 4 : e01747-15.
Blin, K., Shaw, S., Steinke, K., Villebro, R., Ziemert, N., Lee, S.Y., …Weber, T. (2019). antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Research , 47 : W81–W87.
Bomke, C., Rojas, M.C., Gong, F., Hedden, P., & Tudzynski, B. (2008). Isolation and characterization of the gibberellin biosynthetic gene cluster in Sphaceloma manihoticola. Applied and Environmental Microbiology , 74 : 5325–5339.
Bualem, B., Mohamed, B., & Moulay, B. (2015). Salinity influence upon activity of Trichoderma harzianum againstBotrytis cinérea . Asian Journal of Plant Pathology , 9 : 158–166.
Calvert, M.J., Ashton, P.R., & Allemann, R.K. (2002).Germacrene A is a product of the Aristolochene Synthase-mediated conversion of farnesylpyrophosphate to aristolochene. Journal of the American Chemical Society, 124 : 11636–11641.
Calvo, A.M., Wilson, R.A., Bok, J.W., & Keller, N.P. (2002).  Relationship between secondary metabolism and fungal development. Microbiology and Molecular Biology Reviews, 66 : 447-459.
Cane, D.E., Xue, Q., & Fitzsimons, B.C. (1996). Trichodiene synthase. Probing the role of the highly conserved aspartate-rich region by site-directed mutagenesis. Biochemistry , 35 : 12369–12376.
Cardoza, R.E., Malmierca, M.G., Hermosa, M.R., Alexander, N.J., McCormick, S.P., Proctor, R.H., … Gutiérrez, S. (2011).Identification of loci and functional characterization of trichothecene biosynthesis genes in filamentous fungi of the genus Trichoderma. Applied and Environmental Microbiology , 77 : 4867–4877.
Chen, S., Li, H., Chen, Y., Li, S., Xu, J., Guo, H., … Zhang, W. (2019). Three new diterpenes and two new sesquiterpenoids from the endophytic fungus Trichoderma koningiopsis A729.Bioorganic Chemistry , 86 : 368–374.
Chiba, R., Minami, A., Gomi, K., & Oikawa, H. (2013) . Identification of ophiobolin F synthase by a genome mining approach: a sesterterpene synthase from Aspergillus clavatus . Organic Letters , 15 : 594–597.
Contreras-Cornejo, H.A., Macías-Rodríguez, L., del-Val, E., & Larsen, J. (2016). Ecological functions of Trichoderma spp. and their secondary metabolites in the rhizosphere: interactions with plants. FEMS Microbiology Ecology , 92 : fiw036.
Contreras-Cornejo, H.A., Del-Val, E., Macías-Rodríguez, L., Alarcón, A., González-Esquivel, C.E., & Larsen, J. (2018).Trichoderma atroviride , a maize root associated fungus, increases the parasitism rate of the fall armyworm Spodoptera frugiperda by its natural enemy Campoletis sonorensis. Soil Biology and Biochemistry , 122 : 196–202.
Crutcher, F.K., Parich, A., Schuhmacher, R., Mukherjee, P.K., Zeilinger, S., & Kenerley, C.M. (2013). A putative terpene cyclase,vir4 , is responsible for the biosynthesis of volatile terpene compounds in the biocontrol fungus Trichoderma virens. Fungal Genetics and Biology , 56 : 67–77.
De Vries, R.P., Riley, R., Wiebenga, A., Aguilar-Osorio, G., Amillis, S., Uchima, C.A., … Grigoriev, I.V. (2017). Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus. Genome Biology , 18 : 28.
Druzhinina, I.S., Chenthamara, K., Zhang, J., Atanasova, L., Yang, D., Miao, Y., … Kubicek, C.P. (2018). Massive lateral transfer of genes encoding plant cell wall-degrading enzymes to the mycoparasitic fungus Trichoderma from its plant-associated hosts. PLOS Genetics , 14 : e1007322.
Fanelli, F., Liuzzi, V.C., Logrieco, A.F., & Altomare, C. (2018). Genomic characterization of Trichoderma atrobrunneum(T. harzianum species complex) ITEM 908: insight into the genetic endowment of a multi-target biocontrol strain. BMC Genomics , 19 : 662.
Fiorini, L.,Guglielminetti, L., Mariotti, L., Curadi, M., Picciarelli, P., Scartazza, A., … Vannacci, G. (2016).Trichoderma harzianum T6776 modulates a complex metabolic network to stimulate tomato cv. Micro-Tom growth. Plant Soil , 400 : 351–366.
Fountain, J.C., Bajaj, P., Nayak, S.N., Yang, L., Pandey, M.K., Kumar, V., … Guo, B. (2016). Responses of Aspergillus flavus to oxidative stress are related to fungal development regulator, antioxidant enzyme, and secondary metabolite biosynthetic gene expression. Frontiers in Microbiology , 7: 2048.
Gallo, A., Mulè, G., Favilla, M., & Altomare, C. (2004).Isolation and characterisation of a trichodiene synthase homologous gene in Trichoderma harzianum. Physiological and Molecular Plant Pathology , 65 : 11–20.
Gao, Y., Honzatko, R.B., & Peters, R.J. (2012). Terpenoid synthase structures: a so far incomplete view of complex catalysis.Natural Product Reports , 29 : 1153.
Ghisalberti, E.L. (1993). Detection and isolation of bioactive natural products. In: Colegate SM, Molyneux RJ, eds. Bioactive natural products: detection, isolation and structure elucidation. CRC Press, Boca Raton, 15–18.
Guindon, S., Dufayard, J.F., Lefort, V., Anisimova, M., Hordijk, W., & Gascuel O. (2010). New algorithms and methods to estimate Maximum-Likelihood phylogenies: Assessing the performance of PhyML 3.0. Systematic Biology , 59 : 307–321.
Guzmán-Chávez, F., Zwahlen, R.D., Bovenberg, R.A.L., & Driessen, A.J.M. (2018).  Engineering of the filamentous fungusPenicillium chrysogenum as cell factory for natural products. Frontiers in Microbiology, 9 : 2768.
Harman, G.E., Howell, C.R., Viterbo, A., Chet, I., & Lorito, M. (2004). Trichoderma species opportunistic, avirulent plant symbionts. Nature Reviews Microbiology 84 : 377–393.
Hautbergue, T., Jamin, E.L., Debrauwer, L., Puel, O., & Oswald, I.P. (2018). From genomics to metabolomics, moving toward an integrated strategy for the discovery of fungal secondary metabolites. Natural Product Reports , 35 : 147–173.
Hermosa, R., Cardoza, R.E., Rubio, M.B., Gutiérrez, S., & Monte, E. (2014). Secondary metabolism and antimicrobial metabolites ofTrichoderma. In: Vijai GP, Schmoll M, Herrera-Estrella A, Upadhyay RS, Druzhinina I, Tuohy MG, eds. Biotechnology and Biology of Trichoderma , Elsevier, 125–137.
Hidangmayum, A., & Dwivedi, P. (2018). Plant responses toTrichoderma spp. and their tollerance to abiotic stresses: a review. Journal of Pharmacognosy and Phytochemistry E-ISSN: 2278–4136.
Hon, T.M., & Desjardins, A.E. (1992). Isolation and gene disruption of the Tox5 gene encoding trichodiene synthase inGibberella pulicaris . Molecular Plant-Microbe Interactions,5 : 249–256.
Hong, S.Y., Roze, L., & Linz, J. (2013). Oxidative stress-related transcription factors in the regulation of secondary metabolism. Toxins , 5 : 683–702.
Inayati, A., Sulistyowati, L., Aini, L.Q., & Yusnawan, E. (2019). Antifungal activity of volatile organic compounds fromTrichoderma virens. International conference on biology and applied science (ICOBAS) .
Izquierdo-Bueno, I., Moraga, J., Cardoza, R.E., Lindo, L., Hanson, J.R., Gutiérrez, S., & Collado, I.G. (2018). Relevance of the deletion of the Tatri4 gene in the secondary metabolome ofTrichoderma arundinaceum. Organic & Biomolecular Chemistry , 16 : 2955–2965.
Jiao, F., Kawakami, A., & Nakajima, T. (2008). Effects of different carbon sources on trichothecene production and Tri gene expression by Fusarium graminearum in liquid culture. FEMS Microbiology Letters , 285 : 212–219.
Jones, P., Binns, D., Chang, H.Y., Fraser, M., Li, W., McAnulla, C., … Hunter, S. (2014). InterProScan 5: genome-scale protein function classification. Bioinformatics , 30 : 1236–1240.
Jourdier, E., Baudry, L., Poggi-Parodi, D., Vicq, Y., Koszul, R., Margeot, A., … Bidard, F. (2017). Proximity ligation scaffolding and comparison of two Trichoderma reesei strains genomes. Biotechnology for Biofuels , 10 : 151.
Katoh, K., & Standley, D.M. (2013). MAFFT Multiple Sequence Alignment Software Version 7: Improvements in performance and usability.Molecular Biology and Evolution, 30 : 772–780.
Kim, S., Cheong, J.H., & Yoo, J. (1998). Radical cyclization of N-Aziridinylimines 4. Highly efficient synthesis of dl-pentalenene via consecutive carbon-carbon bond formation approach. Synlett , 1998 : 981–982.
Kubicek, C.P., Herrera-Estrella, A., Seidl-Seiboth, V., Martinez, D.A., Druzhinina, I.S., Thon, M., … Grigoriev, I.G. (2011). Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma . Genome Biology , 12 : R40.
Kubicek, C.P., Steindorff, A.S., Chenthamara, K., Manganiello, G., Henrissat, B., Zhang, J., … Druzhinina, I.S. (2019).Evolution and comparative genomics of the most common Trichodermaspecies. BMC Genomics , 20 : 485.
Kushiro, T., Shibuya, M., Masuda, K., & Ebizuka, Y. (2000).Mutational studies on triterpene synthases:  engineering lupeol synthase into β-amyrin synthase. Journal of the American Chemical Society , 122 : 6816–6824.
Li, W.C., Huang, C.H., Chen, C.L., Chuan,g Y.C., Tung, S.Y., & Wang, T.F. (2017). Trichoderma reesei complete genome sequence, repeat-induced point mutation, and partitioning of CAZyme gene clusters. Biotechnology for Biofuels , 10 : 170.
Linnemannstöns, P., Prado, M., Fernández-Martín, R., Tudzynski, B., & Avalos, J. (2002). A carotenoid biosynthesis gene cluster inFusarium fujikuroi : the genes carB and carRA. Molecular Genetics and Genomics , 267 : 593–602.
Linscott, K.B., Niehaus, T.D., Zhuang, X., Bell, S.A., & Chappell, J. (2016). Mapping a kingdom-specific functional domain of squalene synthase. Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids , 1861 : 1049–1057.
Livak, K.J., & Schmittgen, T.D. (2001). Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method. Methods , 25 : 402–408.
Lodeiro, S., Xiong, Q., Wilson, W.K., Ivanova, Y., Smith, M.L., May, G.S., & Matsuda, S.P.T. (2009). Protostadienol biosynthesis and metabolism in the pathogenic fungus Aspergillus fumigatus .Organic Letters , 11 : 1241–1244.
Logemann, J., Schell, J., & Willmitzer, L. (1987). Improved method for the isolation of RNA from plant tissues. Analytical Biochemistry , 163 : 16–20.
Lopez-Gallego, F., Agger, S.A., Abate-Pella, D., Distefano, M.D., & Schmidt-Dannert, C. (2010). Sesquiterpene synthases Cop4 and Cop6 from Coprinus cinereus : Catalytic promiscuity and cyclization of farnesyl pyrophosphate geometric isomers. ChemBioChem , 11 : 1093–1106.
Lorito, M., Farkas, V., Rebuffat, S., Bodo, B., & Kubicek, C.P. (1996). Cell wall synthesis is a major target of mycoparasitic antagonism by Trichoderma harzianum. Journal of Bacteriology , 178 : 6382–6385.
Malmierca, M.G., Barua, J., McCormick, S.P., Izquierdo-Bueno, I., Cardoza, R.E., Alexander, N.J., … Gutiérrez, S. (2015).N ovel aspinolide production by Trichoderma arundinaceumwith a potential role in Botrytis cinerea antagonistic activity and plant defence priming. Environmental Microbiology , 17 : 1103–1118.
Malmierca, M.G., Cardoza, R.E., Alexander, N.J., McCormick, S.P., Collado, I.G., Hermosa, R., … Gutiérrez, S. (2013).Relevance of trichothecenes in fungal physiology: Disruption oftri5 in Trichoderma arundinaceum. Fungal Genetics and Biology , 53 : 22–33.
Malmierca, M.G., McCormick, S.P., Cardoza, R.E., Alexander, N.J., Monte, E., & Gutiérrez, S. (2014). Production of trichodiene byTrichoderma harzianum alters the perception of this biocontrol strain by plants and antagonized fungi. Environmental Microbiology , 17 : 2628–2646.
Marik, T., Urbán, P., Tyagi, C., Szekeres, A., Leitgeb, B., Vágvölgyi, M., … Kredics, L. (2017). Diversity profile and dynamics of peptaibols produced by green mould Trichodermaspecies in interactions with their hosts Agaricus bisporus andPleurotus ostreatus. Chemistry & Biodiversity , 14 : e1700033.
Matarese, F. (2010). Biocontrol of Fusarium Head Bligth: molecular interactions between Trichoderma and mycotoxigenicFusarium . PhD Thesis, University of Pisa, Pisa, Italy.
Matarese, F., Sarrocco, S., Gruber, S., Seidl-Seiboth, V., & Vannacci, G. (2012). Biocontrol of Fusarium head blight: interactions between Trichoderma and mycotoxigenic Fusarium. Microbiology , 158 : 98–106.
Matsuda, Y., Mitsuhashi, T., Lee, S., Hoshino, M., Mori, T., Okada, M., … Abe, I. (2016). Astellifadiene: structure determination by NMR spectroscopy and crystalline sponge method, and elucidation of its biosynthesis. Angewandte Chemie, 128 : 5879–5882.
McCormick, S.P., Alexander, N.J., & Harris, L.J. (2009).CLM1 of Fusarium graminearum encodes a longiborneol synthase required for culmorin production. Applied and Environmental Microbiology , 76 : 136–141.
Miao, F.P., Liang, X.R., Yin, X.L., Wang, G., & Ji, N.Y. (2012). Absolute configurations of unique harziane diterpenes fromTrichoderma species. Organic Letters , 14 : 3815–3817.
Mitsuhashi, T., Rinkel, J., Okada, M., Abe, I., & Dickschat, J.S. (2017). Mechanistic characterization of two chimeric sesterterpene synthases from Penicillium. Chemistry - A European Journal , 23 : 10053–10057.
Mukherjee, P.K., Horwitz, B.A., Herrera-Estrella, A., Schmoll, M., & Kenerley, C.M. (2013). Trichoderma Research in the Genome Era. Annual Review of Phytopathology , 51 : 105–129.
Nakano, C., & Hoshino, T. (2009). Characterization of theRv3377c gene product, a type-B diterpene cyclase, from theMycobacterium tuberculosis H37 genome. ChemBioChem,10 : 2060–2071.
Nakano, C., Okamura, T., Sato, T., Dairi, T., & Hoshino, T. (2005). Mycobacterium tuberculosis H37Rv3377c encodes the diterpene cyclase for producing the halimane skeleton.Chemical Communications , 8 : 1016–1018.
Nicholson, M.J., Koulman, A., Monahan, B.J., Pritchard, B.L., Payne, G.A., & Scott, B. (2009). Identification of two aflatrem biosynthesis gene loci in Aspergillus flavus and metabolic engineering of Penicillium paxilli to elucidate their function. Applied and Environmental Microbiology , 75 : 7469–7481.
Nierman, W.C., Yu, J., Fedorova-Abrams, N.D., Losada, L., Cleveland, T.E., Bhatnagar, D., … Payne, G.A. (2015). Genome sequence of Aspergillus flavus NRRL 3357, a strain that causes aflatoxin contamination of food and feed. Genome Announcements , 3 : e00168-15.
Oikawa, H., Toyomasu, T., Toshima, H., Ohashi, S., Kawaide, H., Kamiya, Y., … Sassa, T. (2001). Cloning and functional expression of cDNA encoding aphidicolan-16β-ol synthase:  a key enzyme responsible for formation of an unusual diterpene skeleton in biosynthesis of aphidicolin. Journal of the American Chemical Society , 123 : 5154–5155.
Okada, M., Matsuda, Y., Mitsuhashi, T., Hoshino, S., Mori, T., Nakagawa, K., … Abe, I. (2016). Genome-based discovery of an unprecedented cyclization mode in fungal sesterterpenoid biosynthesis.Journal of the American Chemical Society , 138 : 10011–10018.
Pachauri, S., Sherkhane, P.D., & Mukherjee, P. (2019).Secondary metabolism in Trichoderma : chemo- and geno- diversity. In: Satyanarayana T, Das SK, Johri BN, eds. Microbial Diversity in Ecosystem Sustainability , Singapore, Springer, 441-456.
Parker, E.J., & Scott, B. (2004). Indole-diterpene biosynthesis in ascomycetous fungi. In: An Z (ed), Handbook of Industrial Mycology. Marcel Dekker, New York, 405–426.
Patil, A.S., Patil, S.R., & Paikrao, H.M. (2016).Trichoderma secondary metabolites: Their biochemistry and possible role in disease management. In: Choudhary DK, Varma A, eds.Microbial-Mediated Induced Systemic Resistance in Plants , Singapore Springer, 69–102.
Piłsyk, S., Perlińska-Lenart, U., Górka-Nieć, W., Graczyk, S., Antosiewicz, B., Zembek, P., … Kruszewska, J.S. (2014).Overexpression of erg20 gene encoding farnesyl pyrophosphate synthase has contrasting effects on activity of enzymes of the dolichyl and sterol branches of mevalonate pathway in Trichoderma reesei. Gene , 544 : 114–122.
Pinedo, C., Wang, C.M., Pradier, J.M., Dalmais, B., Choquer, M., Le Pêcheur, P., … Viaud, M. (2008). Sesquiterpene synthase from the botrydial biosynthetic gene cluster of the phytopathogenBotrytis cinerea. ACS Chemical Biology , 3 : 791–801.
Price, M.N., Dehal, P.S., & Arkin, A.P. (2010). FastTree 2 – Approximately Maximum-Likelihood trees for large alignments. PLoS ONE , 5 : e9490.
Proctor, R.H., McCormick, S.P., Kim, H.S., Cardoza, R.E., Stanley, A.M., Lindo, L … Gutiérrez, S. (2018). Evolution of structural diversity of trichothecenes, a family of toxins produced by plant pathogenic and entomopathogenic fungi. PLOS Pathogens , 14 : e1006946.
Qin, B., Matsuda, Y., Mori, T., Okada, M., Quan, Z., Mitsuhashi, T., Wakimoto, T., & Abe, I. (2015). An unusual chimeric diterpene synthase from Emericella variecolor and its functional conversion into a sesterterpene synthase by domain swapping. Angewandte Chemie , 128 : 1690–1693.
Quin, M.B., Flynn, C.M., & Schmidt-Dannert, C. (2014).  Traversing the fungal terpenome. Natural Products Report , 31 : 1449–1473.
Rai, S., Solanki, M.K., Solanki, A.C., & Surapathrudu, K. (2019). Biocontrol potential of Trichoderma spp.: Current understandings and future outlooks on molecular techniques. In Ansari RA, Mahmood I, eds. Plant Health Under Biotic Stress , Springer, Singapore, 129–160.
Reino, J.L., Guerrero, R.F., Hernandez-Galan, R., & Collado, I.G. (2008). Secondary metabolites from species of the biocontrol agentTrichoderma. Phytochemistry Reviews , 7 : 89–123.
Ronquist, F., & Huelsenbeck, J.P. (2003). MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics,19 : 1572–1574.
Rynkiewicz, M.J., Cane, D.E., & Christianson, D.W. (2001).Structure of trichodiene synthase from Fusarium sporotrichioidesprovides mechanistic inferences on the terpene cyclization cascade.Proceedings of the National Academy of Sciences , 98 : 13543–13548.
Saikia, S., Nicholson, M.J., Young, C., Parker, E.J., & Scott, B. (2008). The genetic basis for indole-diterpene chemical diversity in filamentous fungi. Mycological Research , 112 : 184–199.
Salwan, R., Rialch, N., & Sharma, V. (2019). Bioactive volatile metabolites of Trichoderma : An overview. In: Singh HB, Keswani C, Reddy MS, Sansinenea E, García-Estrada C, eds.Secondary Metabolites of Plant Growth Promoting Rhizomicroorganisms , Singapore, Springer, 87–111.
Sarrocco, S., Matarese, F., Moncini, L., Pachetti, G., Ritieni, A., Moretti, A., & Vannacci, G. (2013b). Biocontrol of Fusarium head blight by spike application of Trichoderma gamsii. Journal of Plant Pathology . S1 : 19–27
Sarrocco, S., Mauro, A., Battilani, P. (2019). Use of competitive filamentous fungi as an alternative approach for mycotoxin risk reduction in staple cereals: State of art and future perspectives.Toxins, 11 : 701.
Sarrocco, S., Esteban, P., Vicente, I., Bernardi, R., Plainchamp, T., Domenichini, S., … Dufresne, M. 2020. Straw competition and wheat root endophytism of Trichoderma gamsii T6085 as useful traits in the biocontrol of Fusarium Head Blight.Phytopathology (submitted)
Sarrocco, S., Moncini, L., Pachetti, G., Moretti, A., Ritieni, A., & Vannacci, G. (2013a). Biological control of Fusarium Head Blight under field conditions. Biocontrol of Plant Pathogens in Sustainable Agriculture , 86 : 95–100.
Schmidhauser, T.J., Lauter, F.R., Schumacher, M., Zhou, W., Russo, V.E.A., & Yanofsky, C. (1994). Characterization of al-2 , the phytoene synthase gene of Neurospora crassa. The Journal of Biological Chemistry , 269 : 12060–12066.
Schmidt-Dannert, C. (2014).  Biosynthesis of terpenoid natural products in fungi. In: Schrader J, Bohlmann J, eds. Biotechnology of Isoprenoids. Advances in Biochemical Engineering/Biotechnology, Singapore Springer, 19–61.
Shaw, J.J., Berbasova, T., Sasaki, T., Jefferson-George, K., Spakowicz, D.J., Dunican, B.F., … Strobel, S.A. (2015).  Identification of a fungal 1,8-cineole synthase fromHypoxylon sp. with specificity determinants in common with the plant synthases. Journal of Biological Chemistry , 290 : 8511–8526.
Shinohara, Y., Takahashi, S., Osada, H., & Koyama, Y. (2016).Identification of a novel sesquiterpene biosynthetic machinery involved in astellolide biosynthesis. Scientific Reports , 6 : 32865.
Shoresh, M., Harman, G.E., Mastouri, F. (2010). Induced systemic resistance and plant responses to fungal biocontrol agents.Annual Review of Phytopathology , 48 : 21–43.
Sishova, E.Y., Di Costanzo, L., Cane, D.E., & Christianson, D.W. (2007). X -ray crystal structure of Aristolochene Synthase from Aspergillus terreus and evolution of templates for the cyclization of farnesyl diphosphate. Biochemistry,46 : 1941–1951.
Song, Y.P., Fang, S.T., Miao, F.P., Yin, X.L., & Ji, N.Y. (2018). Diterpenes and sesquiterpenes from the marine algicolous fungusTrichoderma harzianum X-5. Journal of Natural Products , 81 : 2553–2559.
Starks, C.M. (1997). Structural basis for cyclic terpene biosynthesis by tobacco 5-Epi-aristolochene synthase. Science , 277 : 1815–1820.
Studholme, D.J., Harris, B., Le Cocq, K., Winsbury, R., Perera, V., Ryder, L., … Grant, M. (2013). Investigating the beneficial traits of Trichoderma hamatum GD12 for sustainable agriculture - insights from genomics. Frontiers in Plant Science , 4 : 258.
Tian, G., Deng, X., & Hong, K. (2017). The biological activities of sesterterpenoid-type ophiobolins. Marine Drugs15 : 229.
Tijerino, A., Cardoza, R.E., Moraga, J., Malmierca, M.G., Vicente, F., Aleu, J., … Hermosa, R. (2011a). Overexpression of the trichodiene synthase gene tri5 increases trichodermin production and antimicrobial activity in Trichoderma brevicompactum. Fungal Genetics and Biology , 48 : 285–296.
Tijerino, A., Hermosa, R., Cardoza, R.E., Moraga, J., Malmierca, M.G., Aleu, J., … Gutierrez, S. (2011b). Overexpression of theTrichoderma brevicompactum tri5 gene: Effect on the expression of the trichodermin biosynthetic genes and on tomato seedlings. Toxins , 3 : 1220–1232.
Toyomasu, T., Tsukahara, M., Kaneko, A., Niida, R., Mitsuhashi, W., Dairi, T., … Sassa, T. (2007). Fusicoccins are biosynthesized by an unusual chimera diterpene synthase in fungi. Proceedings of the National Academy of Sciences , 104 : 3084–3088.
Tudzynski, B., Kawaide, H., & Kamiya, Y. (1998). Gibberellin biosynthesis in Gibberella fujikuroi: cloning and characterization of the copalyl diphosphate synthase gene. Current Genetics , 34 : 234–240.
Vinale, F., Sivasithamparam, K., Ghisalberti, E.L., Marra, R., Barbetti, M.J., Li, H., … Lorito, M. (2008). A novel role forTrichoderma secondary metabolites in the interactions with plants. Physiological and Molecular Plant Pathology , 72 : 80–86.
Viterbo, A., Wiest, A., Brotman, Y., Chiet, I., & Kenerley, C. (2007). The 18mer peptaibols from Trichoderma virens elicit plant defence responses. Molecular Plant Pathology, 8 : 737–746.
Wendt, K.U., & Schulz, G.E. (1998). Isoprenoid biosynthesis: manifold chemistry catalyzed by similar enzymes.Structure , 6 :127-133.
Whelan, S., & Goldman, N. (2001). A general empirical model of protein evolution derived from multiple protein families using a Maximum-Likelihood approach. Molecular Biology and Evolution , 18 : 691–699.
Wiemann, P., Sieber, C.M.K., von Bargen, K.W., Studt, L., Niehaus, E.M., Espino, J.J., … Tudzynski, B. (2013). Deciphering the cryptic genome: genome-wide analyses of the rice pathogenFusarium fujikuroi reveal complex regulation of secondary metabolism and novel metabolites. PLOS Pathogens , 9 : e1003475.
Xiao, G., Ying, S.H., Zheng, P., Wang, Z.L., Zhang, S., Xie, X.Q., … Feng, M.G. (2012). Genomic perspectives on the evolution of fungal entomopathogenicity in Beauveria bassiana. Scientific Reports , 2 : 483.
Yang, D., Pomraning, K., Kopchinskiy, A., Aghcheh, R.K., Atanasova, L., Chenthamara, K., … Druzhinina, I.S. (2015).Genome sequence and annotation of Trichoderma parareesei , the ancestor of the cellulase producer Trichoderma reesei. Genome Announcements , 3 : e00885-15.
Young, C.A., Felitti, S., Shields, K., Spangenberg, G., Johnson, R.D., Bryan, G.T., … Scott, B. (2006).  A complex gene cluster for indole-diterpene biosynthesis in the grass endophyteNeotyphodium lolii. Fungal Genetics and Biology , 43 : 679–693.
Young, C., McMillan, L., Telfer, E., & Scott, B. (2001).Molecular cloning and genetic analysis of an indole-diterpene gene cluster from Penicillium paxilli. Molecular Microbiology , 39 : 754–764.
Yu, J.H., & Keller, N. (2005). Regulation of secondary metabolism in filamentous fungi. Annual Review of Phytopathology,43 : 437–458.
Zapparata, A., Da Lio, D., Somma, S., Vicente Muñoz, I., Malfatti, L., Vannacci, G., … Sarrocco, S. (2017). Genome sequence of Fusarium graminearum ITEM 124 (ATCC 56091), a mycotoxigenic plant pathogen. Genome Announcements , 5 : e01209-17.
Zeilinger, S., Gruber, S., Bansal, R., & Mukherjee, P.K. (2016). Secondary metabolism in Trichoderma – Chemistry meets genomics. Fungal Biology Reviews , 30 : 74–90.
Zhao, D., Yang, L., Shi, T., Wang, C., Shao, C., & Wang, C. (2019).  Potent phytotoxic harziane diterpenes from a soft coral-derived strain of the fungus Trichoderma harzianum  XS-20090075. Scientific Reports , 9 :  13345.
Zhao, L., & Zhang, Y. (2015). Effects of phosphate solubilization and phytohormone production of Trichoderma asperellum Q1 on promoting cucumber growth under salt stress. Journal of Integrative Agriculture , 14 : 1588–1597.
Zhou, J.S., Ji, S.L., Ren, M.F., He, Y.L., Jing, X.R., & Xu, J.W. (2014). Enhanced accumulation of individual ganoderic acids in a submerged culture of Ganoderma lucidum by the overexpression of squalene synthase gene. Biochemical Engineering Journal , 90 : 178–183.