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



Kathamuthu GokulRaj1, Natesan Sundaresan1, Enthai Jagan Ganeshan1, Pandi Rajapriya2, Johnpaul Muthumary3, Jayavel Sridhar4 & Mohan Pandi1*



1Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Madurai 21, Tamil Nadu, India; 2Department of Microbial Technology, School of Biological Sciences, Madurai Kamaraj University, Madurai 21, Tamil Nadu, India; 3Centre for Advanced Studies in Botany, University of Madras, Guindy Campus, Chennai 25, Tamil Nadu, India.; 4Department of Biotechnology (DDE), Madurai Kamaraj University, Madurai 21, Tamil Nadu, India


Email,; *Corresponding author


Article Type




Received May 13, 2014; Accepted May 23, 2014; Published June 30, 2014



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



Endophytes, ITS, MEGA 5.1, ProfDistS, Sequence-secondary structure, 4SALE.



GokulRaj  et al Bioinformation 10(6): 320-328 (2014)

Edited by

P Kangueane






Biomedical Informatics



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