Assessment of the endochitinase (ech42) Protein-Coding Gene as a DNA Barcode for Species Delimitation and Phylogenetic Reconstruction in Trichoderma

Accurate species identification is a prerequisite for deciphering the ecological adaptation, evolutionary diversification, and functional potential of Trichoderma species. It is providing a foundation for understanding their roles in host interactions, environmental fitness, and biocontrol applications. In this study, the protein-coding gene of endochitinase 42 kDa (ech42) was evaluated as a DNA barcode for species delimitation and phylogenetic reconstruction in Trichoderma genus. Phylogenetic inferences were drawn from eight local isolates representing four Trichoderma species. Sequence alignment of the ech42 gene generated a dataset of approximately 850 bp, providing sufficient phylogenetically informative characters for species-level discrimination. Phylogenetic analyses revealed that the ech42 marker consistently resolved all four species, with bootstrap support of 100%. Physicochemical and three-dimensional structural analyses of ech42 gene revealed that their amino acid numbers ranged from 278 to 283 residues in Trichoderma species and T. virens exhibited the most hydrophilic protein, with a GRAVY value of −0.303. These findings demonstrate that the ech42 gene possesses significant potential as a complementary DNA barcode for Trichoderma species identification and phylogenetic studies.