Phylogenetic reconstruction of endophytic fungal isolates using internal transcribed spacer 2 (ITS2) region

Endophytic fungi are inhabitants of plants, living most part of their lifecycle asymptomatically which mainly confer protection andecological advantages to the host plant. In this present study, 48 endophytic fungi were isolated from the leaves of three medicinalplants and characterized based on ITS2 sequence – secondary structure analysis. ITS2 secondary structures were elucidated withminimum free energy method (MFOLD version 3.1) and consensus structure of each genus was generated by 4SALE. ProfDistSwas used to generate ITS2 sequence structure based phylogenetic tree respectively. Our elucidated isolates were belonging toAscomycetes family, representing 5 orders and 6 genera. Colletotrichum/Glomerella spp., Diaporthae/Phomopsis spp., and Alternariaspp., were predominantly observed while Cochliobolus sp., Cladosporium sp., and Emericella sp., were represented by singletons. Theconstructed phylogenetic tree has well resolved monophyletic groups with >50% bootstrap value support. Secondary structuresbased fungal systematics improves not only the stability; it also increases the precision of phylogenetic inference. Above ITS2 basedphylogenetic analysis was performed for our 48 isolates along with sequences of known ex-types taken from GenBank whichconfirms the efficiency of the proposed method. Further, we propose it as superlative marker for reconstructing phylogeneticrelationships at different taxonomic levels due to their lesser length.