The Current State of Trichoderma Taxonomy and Species Identification

Abstract

AbstractBefore the introduction of molecular techniques, the taxonomy of Trichoderma consisted of several dozen species defined based on their morphology, biogeography, and ecophysiology. However, the last two decades have resulted in the rapid expansion of species diversity in the genus. Currently, the genus Trichoderma has at least 469 species names, among which 382 are currently valid. Fourteen species could not be characterized molecularly, but 365 were DNA barcoded for at least one but more frequently several DNA loci. The identification of Trichoderma species is an intricate and laborious task that requires a background in mycology, molecular biological skills, training in molecular evolution, and in-depth knowledge of taxonomic literature. The contemporary diversity of Trichoderma spp. cannot be identified via automated sequence similarity searches (such as NCBI BLAST or MIST BLAST) or oligonucleotide DNA barcodes such as TrichOKEY. All molecular identification results require in silico validation and biological verification. Similarly, Trichoderma spp. cannot be identified by phylogenetic analysis without considering the sequence similarity values to the complete set of closely related species. Due to the high number of cryptic and closely related species, the accurate molecular identification of Trichoderma species currently requires the analysis of at least three DNA barcodes: ITS, tef1, and rpb2. However, the sets of these three loci are available for only 273 species. Considering that many of these species were characterized by incomplete reference sequences or shared tef1 or rpb2 phylotypes with other species, unambiguous identification is possible for not more than 224 species that comprise 60% of the total number of species. The molecular identification of 40% of contemporary Trichoderma species is only possible with a certain degree of ambiguity; therefore, the choice should be made either toward high accuracy (lower taxonomic resolution) or precision (lower accuracy). The community of Trichoderma taxonomy providers is therefore invited to the discussion of the coordinated measures toward the improvement of this unfortunate taxonomic situation in the genus.KeywordsThe CodeCommunityDiversityDNA barcoding Hypocrea ICTTMolecular identificationNomenclatureSpeciationSpecies