An insight into mitochondrial genomes of Trichoderma afroharzianum strains: a comparative and evolutionary analysis

Abstract Trichoderma afroharzianum (Ascomycota: Hypocreales) is known as an important mycoparasite and biocontrol fungus and feeds on fungal material by parasitizing other fungi. Recent studies indicate that this species is also an ear rot pathogen in Europe. Here, the complete mitochondrial genome (mitogenome) of three T. afroharzianum strains was sequenced using next generation sequencing and comparatively characterised by the reported Trichoderma mitogenomes. T. afroharzianum mitogenomes were varying between 29,511 bp and 29,517 bp in length, with an average A + T content of 72.32%. These relatively compact mitogenomes contain 14 core PCGs, 22 tRNAs, two rRNAs, one gene encoding the ribosomal protein S3 and three or four genes including conserved domains for the homing endonucleases (HEGs; GIY-YIG type and LAGLIDADG type). All PCGs are initiated by ATG codons, except for atp8, and all are terminated with TAA as a stop codon. A significant correlation was observed between nucleotide composition and codon preference. Four introns belonging to the group I intron were predicted, accounting for about 14.54% of size of the mitogenomes. Phylogenetic analyses confirmed the positions of T. afroharzianum strains within the genus of Trichoderma and supported a sister relationship between T. afroharzianum and T. harzianum + T. lixii. The recovered trees also supported the monophyly of Nectriaceae, Bionectriaceae, Hypocreales incertea sedis, Cordycipitaceae and Hypocreaceae. However, Ophiocordycipitaceae and Clavicipitaceae were found to be paraphyletic.