[Aldrich J., Cullis C.A. 1993. RAPD analysis in flax: optimization of yield and reproducibility using KlenTaq 1 DNA polymerase, Chelex 100, and gel purification of genomic DNA. Plant Molecular Biology Reporter 11: 128-141. DOI: 10.1007/BF02670471.10.1007/BF02670471]Search in Google Scholar
[Altschul S.F., Madden T.L., Schäffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research 25: 3389-3402. DOI: 10.1093/nar/25.17.3389.10.1093/nar/25.17.3389]Search in Google Scholar
[Atanasova L., Druzhinina I.S., Jaklitsch W.M. 2013. Two hundred Trichoderma species recognized on the basis of molecular phylogeny. In: Mukherjee P.K., Horwitz B.A., Singh U.S., Mukherjee M., Schmoll M. (Eds.), Trichoderma: biology and applications. CABI, Wallingford, UK, pp. 10-42. DOI: 10.1079/9781780642475.0010.10.1079/9781780642475.0010]Search in Google Scholar
[Benítez T., Rincón A.M., Limón M.C., Codón A.C. 2004. Biocontrol mechanisms of Trichoderma strains. International Microbiology 7: 249-260.]Search in Google Scholar
[Błaszczyk L., Popiel D., Chełkowski J., Koczyk G., Samuels G.J., Sobieralski K., Siwulski M. 2011. Species diversity of Trichoderma in Poland. Journal of Applied Genetics 52: 233-243. DOI: 10.1007/s13353-011-0039-z.10.1007/s13353-011-0039-z]Search in Google Scholar
[Carbone I., Kohn L.M. 1999. A method for designing primer sets for speciation studies in filamentous ascomycetes. Mycologia 91: 553-556. DOI: 10.2307/3761358.10.2307/3761358]Search in Google Scholar
[Chaverri P., Branco-Rocha F., Jaklitsch W.M., Gazis R.O., Degenkolb T., Samuels G.J. 2015. Systematics of the Trichoderma harzianum species complex and the re-identification of commercial biocontrol strains. Mycologia 107: 558-590. DOI: 10.3852/14-147.10.3852/14-147]Search in Google Scholar
[Chaverri P., Castlebury L.A., Samuels G.J., Geiser D.M. 2003. Multilocus phylogenetic structure within the Trichoderma harzianum/Hypocrea lixii complex. Molecular Phylogenetics and Evolution 27: 302-313. DOI: 10.1016/S1055-7903(02)00400-1.10.1016/S1055-7903(02)00400-1]Search in Google Scholar
[Chaverri P., Gazis R.O., Samuels G.J. 2011. Trichoderma amazonicum, a new endophytic species on Heveabrasiliensis and H. guianensis from the Amazon basin. Mycologia 103: 139-151. DOI: 10.3852/10-078.10.3852/10-07820943534]Search in Google Scholar
[Cooke D.E.L., Duncan J.M. 1997. Phylogenetic analysis of Phytophthora species based on ITS1 and ITS2 sequences of the ribosomal RNA gene repeat. Mycological Research 101: 667-677. DOI: 10.1017/S0953756296003218.10.1017/S0953756296003218]Search in Google Scholar
[Darriba D., Taboada G.L., Doallo R., Posada D. 2012. jModelTest 2: more models, new heuristics and parallel computing. Nature Methods 9: 772. DOI: 10.1038/nmeth.2109.10.1038/nmeth.2109459475622847109]Search in Google Scholar
[Dodd S.L., Lieckfeldt E., Samuels G.J. 2003. Hypocrea atroviridis sp. nov., the teleomorph of Trichoderma atroviride. Mycologia 95: 27-40. DOI: 10.2307/3761959.10.2307/3761959]Search in Google Scholar
[Druzhinina I.S., Kopchinskiy A.G., Komoń M., Bissett J., Szakacs G., Kubicek C.P. 2005. An oligonucleotide barcode for species identification in Trichoderma and Hypocrea. Fungal Genetics and Biology 42: 813-828. DOI: 10.1016/j.fgb.2005.06.007.10.1016/j.fgb.2005.06.00716154784]Search in Google Scholar
[Druzhinina I.S., Kubicek C.P., Komoń-Żelazowska M., Mulaw T.B., Bissett J. 2010. The Trichoderma harzianum demon: complex speciation history resulting in coexistence of hypothetical biological species, recent agamospecies and numerous relict lineages. BMC Evolutionary Biology 10: 94. DOI: 10.1186/1471-2148-10-94.10.1186/1471-2148-10-94285814720359347]Search in Google Scholar
[Fekete C., Weszely T., Hornok L. 1996. Assignment of a PCR-amplified chitinase sequence cloned from Trichodermahamatum to resolved chromosomes of potential biocontrol species of Trichoderma. FEMS Microbiology Letters 145: 385-391. DOI: 10.1111/j.1574-6968.1996.tb08605.x.10.1111/j.1574-6968.1996.tb08605.x8978093]Search in Google Scholar
[Gal-Hemed I., Atanasova L., Komoń-Żelazowska M., Druzhinina I.S., Viterbo A., Yarden O. 2011. Marine isolates of Trichoderma spp. as potential halotolerant agents of biological control for arid-zone agriculture. Applied and Environmental Microbiology 77: 5100-5109. DOI: 10.1128/AEM.00541-11.10.1128/AEM.00541-11314743021666030]Search in Google Scholar
[Gazis R., Chaverri P. 2010. Diversity of fungal endophytes in leaves and stems of wild rubber trees (Heveabrasiliensis) in Peru. Fungal Ecology 3: 240-254. DOI: 10.1016/j.funeco.2009.12.001.10.1016/j.funeco.2009.12.001]Search in Google Scholar
[Harman G.E. 2006. Overview of mechanisms and uses of Trichoderma spp. Phytopathology 96: 190-194. DOI: 10.1094/PHYTO-96-0190.10.1094/PHYTO-96-019018943924]Search in Google Scholar
[Harman G.E., Howell C.R., Viterbo A., Chet I., Lorito M. 2004. Trichoderma species – opportunistic, avirulent plant symbionts. Nature Reviews Microbiology 2: 43-56. DOI: 10.1038/nrmicro797.10.1038/nrmicro79715035008]Search in Google Scholar
[Hermosa M.R., Grondona I., Iturriaga E.A., Diaz-Minguez J.M., Castro C., Monte E., Garcia-Acha I. 2000. Molecular characterization and identification of biocontrol isolates of Trichoderma spp. Applied and Environmental Microbiology 66: 1890-1898. DOI: 10.1128/AEM.66.5.1890-1898.2000.10.1128/AEM.66.5.1890-1898.200010142910788356]Search in Google Scholar
[Hermosa R., Rubio M.B., Cardoza R.E., Nicolás C., Monte E., Gutiérrez S. 2013. The contribution of Trichoderma to balancing the costs of plant growth and defense. International Microbiology 16: 69-80. DOI: 10.2436/20.1501.01.181.]Search in Google Scholar
[Hoyos-Carvajal L., Orduz S., Bissett J. 2009. Genetic and metabolic biodiversity of Trichoderma from Colombia and adjacent neotropic regions. Fungal Genetics and Biology 46: 615-631. DOI: 10.1016/j.fgb.2009.04.006.10.1016/j.fgb.2009.04.00619439189]Search in Google Scholar
[Jaklitsch W.M. 2011. European species of Hypocrea part II: species with hyaline ascospores. Fungal Diversity 48: 1-250. DOI: 10.1007/s13225-011-0088-y.10.1007/s13225-011-0088-y318978921994484]Search in Google Scholar
[Jaklitsch W.M., Samuels G.J., Dodd S.L., Lu B.S., Druzhinina I.S. 2006. Hypocrea rufa/Trichoderma viride: a reassessment, and description of five closely related species with and without warted conidia. Studies in Mycology 56: 135-177. DOI: 10.3114/sim.2006.56.04.10.3114/sim.2006.56.04210473518490991]Search in Google Scholar
[Jaklitsch W.M., Samuels G.J., Ismaiel A., Voglmayr H. 2013. Disentangling the Trichoderma viridescens complex. Persoonia 31: 112-146. DOI: 10.3767/003158513X672234.10.3767/003158513X672234390404624761039]Search in Google Scholar
[Jaklitsch W.M., Voglmayr H. 2015. Biodiversity of Trichoderma (Hypocreaceae) in Southern Europe and Macaronesia. Studies in Mycology 80: 1-87. DOI: 10.1016/j.simyco.2014.11.001.10.1016/j.simyco.2014.11.001477979526955191]Search in Google Scholar
[Kancelista A., Tril U., Stempniewicz R., Piegza M., Szczech M., Witkowska D. 2013. Application of lignocellulosic waste materials for the production and stabilization of Trichoderma biomass. Polish Journal of Environmental Studies 22: 1083-1090.]Search in Google Scholar
[Kindermann J., El-Ayouti Y., Samuels G.J., Kubicek C.P. 1998. Phylogeny of the genus Trichoderma based on sequence analysis of the internal transcribed spacer region 1 of the rDNA cluster. Fungal Genetics and Biology 24: 298-309. DOI: 10.1006/fgbi.1998.1049.10.1006/fgbi.1998.10499756711]Search in Google Scholar
[Komoń-Żelazowska M., Bissett J., Zafari D., Hatvani L., Manczinger L., Woo S., Lorito M., Kredics L., Kubicek C.P., Druzhinina I.S. 2007. Genetically closely related but phenotypically divergent Trichoderma species cause green mold disease in oyster mushroom farms worldwide. Applied and Environmental Microbiology 73: 7415-7426. DOI: 10.1128/AEM.01059-07.10.1128/AEM.01059-07216820217827333]Search in Google Scholar
[Kopchinskiy A., Komoń M., Kubicek C.P., Druzhinina I.S. 2005. TrichoBLAST: A multilocus database for Trichoderma and Hypocrea identifications. Mycological Research 109: 658-660. DOI: 10.1017/S0953756205233397.10.1017/S095375620523339716080389]Search in Google Scholar
[Kredics L., Hatvani L., Naeimi S., Körmöczi P., Manczinger L., Vágvölgyi C., Druzhinina I. 2014. Biodiversity of the genus Hypocrea/Trichoderma in different habitats. In: Gupta V.K., Schmoll M., Herrera-Estrella A., Upadhyay R.S., Druzhinina I., Tuohy M.G. (Eds.), Biotechnology and biology of Trichoderma. Elsevier, Amsterdam, pp. 3-24. DOI: 10.1016/B978-0-444-59576-8.00001-1.10.1016/B978-0-444-59576-8.00001-1]Search in Google Scholar
[Kullnig C.M., Krupica T., Woo S.L., Mach R.L., Rey M., Benítez T., Lorito M., Kubicek C.P. 2001. Confusion abounds over identities of Trichoderma biocontrol isolates. Mycological Research 105: 769-772. DOI: 10.1017/S0953756201229967.10.1017/S0953756201229967]Search in Google Scholar
[Kullnig-Gradinger C.M., Szakacs G., Kubicek C.P. 2002. Phylogeny and evolution of the genus Trichoderma: a multigene approach. Mycological Research 106: 757-767. DOI: 10.1017/S0953756202006172.10.1017/S0953756202006172]Search in Google Scholar
[Longa C.M.O., Savazzini F., Tosi S., Elad Y., Pertot I. 2009. Evaluating the survival and environmental fate of the biocontrol agent Trichoderma atroviride SC1 in vineyards in northern Italy. Journal of Applied Microbiology 106: 1549-1557. DOI: 10.1111/j.1365-2672.2008.04117.x.10.1111/j.1365-2672.2008.04117.x19210568]Search in Google Scholar
[López-Quintero C.A., Atanasova L., Franco-Molano A.E., Gams W., Komoń-Żelazowska M., Theelen B., Müller W.H., Boekhout T., Druzhinina I. 2013. DNA barcoding survey of Trichoderma diversity in soil and litter of the Colombian lowland Amazonian rainforest reveals Trichoderma strigosellum sp. nov. and other species. Antonie van Leeuwenhoek, Journal of Microbiology 104: 657-674. DOI: 10.1007/s10482-013-9975-4.10.1007/s10482-013-9975-4382423823884864]Search in Google Scholar
[Monfil V.O., Casas-Flores S. 2014. Molecular mechanisms of biocontrol in Trichoderma spp. and their applications in agriculture. In: Gupta V.K., Schmoll M., Herrera-Estrella A., Upadhyay R.S., Druzhinina I., Tuohy M.G. (Eds.), Biotechnology and biology of Trichoderma. Elsevier, Amsterdam, pp. 429-453. DOI: 10.1016/B978-0-444-59576-8.00032-1.10.1016/B978-0-444-59576-8.00032-1]Search in Google Scholar
[Mulaw T.B., Kubicek C.P., Druzhinina I.S. 2010. The rhizosphere of Coffea arabica in its native highland forests of Ethiopia provides a niche for a distinguished diversity of Trichoderma. Diversity 2: 527-549. DOI: 10.3390/d2040527.10.3390/d2040527]Search in Google Scholar
[Ronquist F., Teslenko M., van der Mark P., Ayres D.L., Darling A., Höhna S., et al. 2012. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology 61: 539-542. DOI: 10.1093/sysbio/sys029.10.1093/sysbio/sys029332976522357727]Search in Google Scholar
[Samuels G.J., Dodd S.L., Lu B.S., Petrini O., Schroers H.J., Druzhinina I.S. 2006. The Trichoderma koningii aggregate species. Studies in Mycology 56: 67-133. DOI: 10.3114/sim.2006.56.03.10.3114/sim.2006.56.03210473318490990]Search in Google Scholar
[Skoneczny D., Oskiera M., Szczech M., Bartoszewski G. 2015. Genetic diversity of Trichoderma atroviride strains collected in Poland and identification of loci useful in detection of within-species diversity. Folia Microbiologica 60: 297-307. DOI: 10.1007/s12223-015-0385-z.10.1007/s12223-015-0385-z444548525791292]Search in Google Scholar
[Smolińska U., Gołębiewska E., Kowalska B., Kowalczyk W., Szczech M. 2014a. Materiały odpadowe jako nośniki antagonistycznych grzybów Trichoderma. Inżynieria i Ochrona Środowiska 17: 5-20.]Search in Google Scholar
[Smolińska U., Kowalska B., Kowalczyk W., Szczech M. 2014b. The use of agro-industrial wastes as carriers of Trichoderma fungi in the parsley cultivation. Scientia Horticulturae 179: 1-8. DOI: 10.1016/j.scienta.2014.08.023.10.1016/j.scienta.2014.08.023]Search in Google Scholar
[Stewart A., Hill R. 2014. Applications of Trichoderma in plant growth promotion. In: Gupta V.K., Schmoll M., Herrera-Estrella A., Upadhyay R.S., Druzhinina I., Tuohy M.G. (Eds.), Biotechnology and biology of Trichoderma. Elsevier, Amsterdam, pp. 415-428. DOI: 10.1016/b978-0-444-59576-8.00031-x.10.1016/B978-0-444-59576-8.00031-X]Search in Google Scholar
[Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., Higgins D.G. 1997. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research 25: 4876-4882. DOI: 10.1093/nar/25.24.4876.10.1093/nar/25.24.48761471489396791]Search in Google Scholar
[Vandroemme J., Baeyen S., Van Vaerenbergh J., De Vos P., Maes M. 2008. Sensitive real-time PCR detection of Xanthomonas fragariae in strawberry plants. Plant Pathology 57: 438-444. DOI: 10.1111/j.1365-3059.2007.01813.x.10.1111/j.1365-3059.2007.01813.x]Search in Google Scholar
[White T.J., Bruns T., Lee S., Taylor J. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis M.A., Gelfand D.H., Sninsky J.J., White T.J. (Eds.), PCR protocols: a guide to methods and applications. Academic Press, San Diego, CA, pp. 315-322. DOI: 10.1016/b978-0-12-372180-8.50042-1.10.1016/B978-0-12-372180-8.50042-1]Search in Google Scholar