Molecular Taxonomy and Multigene Phylogeny of Filamentous Fungi

The field of fungal research is experiencing a paradigm shift with respect to technological advancement; however, the mainstay for any advanced research lies in accurate species delimitation. Identification of fungi mainly involves morphological features, which are not always produced in culture and are sometimes variable, which renders identification difficult. Therefore, morphology-based taxonomic approach, though considered indispensable, cannot completely be relied upon because of ambiguity in fungal identification. The DNA-based molecular approaches have proven extremely valuable to mycological venture like species identification, taxonomic classification, and phylogenetic studies. The use of nuclear ribosomal gene, i.e. ITS along with other gene markers (SSU, LSU, RPB1, RPB2, tef1, cal, and tub2, etc.), has been recommended for fungal species level identification and phylogenetic studies. However, the choice of gene target is variable among different groups of fungi. One has to go through multiple research articles, so as to find out the recommended gene targets and their PCR cycling conditions for their fungal group of interest. Therefore, we assembled all the required protocols at one place, starting from fungal DNA isolation, list of recommended gene targets for identification and phylogeny (for selected and most common fungal pathogens), their primer names, sequences and PCR cycling conditions, DNA PCR product purification, and DNA sequencing. We have also briefed about sequence analysis, fungal databases, methodologies, and softwares used for construction of phylogenetic trees. This chapter would be a one stop solution for every researcher especially for the beginners, who is working in the field of taxonomy, phylogeny and evolution of fungi.