Evolution of mycoparasitism in Hypocreales fungi through phylogenomic approach

Abstract

A profound affinity to mycotrophy, i.e. the ability to antagonize, parasitize or even kill a broad range of other fungi including closely related Ascomycota, remains to be the major ecological descriptor of the genus Trichoderma. The pilot phylogenomic analysis of the first three genomes of Trichodema, T. atroviride, T. reesei and T. virens, showed that T. atroviride most closely resembles the ancestral state of the genus, while T. reesei is the most derived taxon from these three. In this thesis, we present the first genus-wide phylogenomics of the genus Trichoderma combining the previously available materials with the data from the seven newly Trichoderma sequenced genomes from T. harzianum, T. guizhouense NJAU 4742, T. asperellum, T. longibrachiatum, T. parareesei C.P.K. 717, T. -afroharzianum- nom. prov. TUCIM 4803 and T. citrinoviride IMI 232088. We have retrieved, manually curated and aligned 100 orthologous proteins from 24 Hypocreales genomes that are currently available. A multi-gene maximum likelihood phylogram is created with MSA constituting 47,655 amino acid residues. This analysis of 24 Hypocreales genomes allowed us to detect the relatively ancient origin of the genus that essentially predates the divergence time for numerous families within the order. Simultaneously, evolutionary position of Escovopsis weberi CC031208-10, a parasite of fungal gardens cultivated by leaf-cutting ants of tribe Attini, namely leaf-cutting ants (Atta and Acromyrmex) is also revealed. We have also retrieved, manually curated and aligned 100 transcripts from 18 of the 24 Hypocrales genomes and created a maximum likelihood phylogram to compare the topologies with our protein phylogram. The transcripts phylogram is based on a MSA constituting 102,317 nucleic acids. Random selection of highly conserved 27 genes out of the 100 transcripts MSA of 18 genomes, followed by single-gene phylogenetic analysis involving 19 Hypocreales, revealed the evolutionary position of recently sequenced genome; Trichoderma hamatum GD 12. Ecophysiological studies are carried out to study and compare opportunistic, mycotrophic and mycoparasitic capabilities among Trichoderma species and also with species of related genera from the family Hypocreaceae, such as Escovopsis weberi. Protocrea pallida, Emericellopsis alkaline, Hypomyces aurantiacus and Simplicillium sp. We demonstrate the unique combination of ecological versatility and high environmental opportunism of the genus Trichoderma that probably is the major feature that distinguishes these fungi from next genetic neighbors.