Fungi of the genus Trichoderma exhibit high genetic diversity and can thus be utilized in a large range of biotechnological applications. While Trichoderma reesei is the primary source of industrial enzymatic cocktails, Trichoderma atroviride and Trichoderma harzianum are widely used as commercial biocontrol agents against plant diseases. Recently, T. harzianum IOC-3844 (Th3844) and T. harzianum CBMAI-0179 (Th0179) demonstrated great potential in the enzymatic conversion of lignocellulose into fermentable sugars. Despite such potential, the genomes of both hydrolytic strains remain unclear. Herein, we performed whole-genome sequencing and assembly of Th3844 and Th0179 strains. To assess the genetic diversity within the genus Trichoderma, the results of both strains were compared with those from T. atroviride CBMAI-00020 (Ta0020) and T. reesei CBMAI-0711 (Tr0711). The resulting assembly revealed a total length of 40 Mb, (Th3844), 39 Mb (Th0179), 36 Mb (Ta0020), and 32 Mb (Tr0711), in which 10,786 (Th3844), 11,322 (Th0179), 10,082 (Ta0020), and 8,796 (Tr0711) genes were predicted. Then, the annotation of the predicted CDS sequences from the evaluated strain genes revealed 413 (Th3844), 413 (Th0179), 377 (Ta0020), and 329 (Tr0711) CAZymes. The orthology analysis revealed 18,349 orthogroups, which encompassed 95% of the total genes, 3,378 orthogroups with all species present, and 408 species-specific orthogroups. A genome-wide phylogenetic analysis modeled from the 1,864 single-copy orthogroups provided details on the relationship of the newly sequenced species with other Trichoderma and with more evolutionarily distant genera. Structural variants revealed genomic rearrangements between Th3844, Th0179, Ta0020, and Tr0711 with the T. reesei QM6a reference genome as well as the functional effects of such variants on the evaluated strains. In conclusion, the findings presented herein allow the genetic diversity of the evaluated strains, including those from the same species, to be viewed, offering opportunities to further explore such fungal genomes in future biotechnological and industrial applications.
