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Background  So far, biocontrol agent selection has been performed mainly by time consuming in vitro confrontation tests followed by extensive trials in greenhouse and field. An alternative approach is offered by application of high-throughput techniques, which allow extensive screening and comparison among strains for desired genetic traits. In the genus  Trichoderma , the past assignments of particular features or strains to one species need to be reconsidered according to the recent taxonomic revisions. Here we present the genome of a biocontrol strain formerly known as  Trichoderma harzianum  ITEM 908, which exhibits both growth promoting capabilities and antagonism against different fungal pathogens, including  Fusarium graminearum ,  Rhizoctonia solani , and the root-knot nematode  Meloidogyne incognita . By genomic analysis of ITEM 908 we investigated the occurrence and the relevance of genes associated to biocontrol and stress tolerance, providing a basis for future investigation aiming to unravel the complex relationships between genomic endowment and exhibited activities of this strain.    Results  The MLST analysis of  ITS-TEF1  concatenated datasets reclassified ITEM 908 as  T. atrobrunneum , a species recently described within the  T. harzianum  species complex and phylogenetically close to  T. afroharzianum  and  T. guizhouense . Genomic analysis revealed the presence of a broad range of genes encoding for carbohydrate active enzymes (CAZYmes), proteins involved in secondary metabolites production, peptaboils, epidithiodioxopiperazines and siderophores potentially involved in parasitism, saprophytic degradation as well as in biocontrol and antagonistic activities. This abundance is comparable to other  Trichoderma  spp. in the  T. harzianum  species complex, but broader than in other biocontrol species and in the species  T. reesei , known for its industrial application in cellulase production. Comparative analysis also demonstrated similar genomic organization of major secondary metabolites clusters, as in other  Trichoderma  species.    Conclusions  Reported data provide a contribution to a deeper understanding of the mode of action and identification of activity-specific genetic markers useful for selection and improvement of biocontrol strains. This work will also enlarge the availability of genomic data to perform comparative studies with the aim to correlate phenotypic differences with genetic diversity of  Trichoderma  species.    Electronic supplementary material  The online version of this article (10.1186/s12864-018-5049-3) contains supplementary material, which is available to authorized users.

bmc genomics

Genomic characterization of Trichoderma atrobrunneum (T. harzianum species complex) ITEM 908: insight into the genetic endowment of a multi-target biocontrol strain