title: Phylogenetic reconstruction of endophytic fungal isolates using internal transcribed spacer 2 (ITS2) region.
abstract: 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.
authors.affiliation: Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Madurai - 21, Tamil Nadu, India.
authors.forename: Kathamuthu
authors.initials: K
authors.lastname: GokulRaj
authors.affiliation: Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Madurai - 21, Tamil Nadu, India.
authors.forename: Natesan
authors.initials: N
authors.lastname: Sundaresan
authors.affiliation: Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Madurai - 21, Tamil Nadu, India.
authors.forename: Enthai Jagan
authors.initials: EJ
authors.lastname: Ganeshan
authors.affiliation: Department of Microbial Technology, School of Biological Sciences, Madurai Kamaraj University, Madurai - 21, Tamil Nadu,India.
authors.forename: Pandi
authors.initials: P
authors.lastname: Rajapriya
authors.affiliation: Centre for Advanced Studies in Botany, University of Madras, Guindy Campus, Chennai - 25, Tamil Nadu, India.
authors.forename: Johnpaul
authors.initials: J
authors.lastname: Muthumary
authors.affiliation: Department of Biotechnology (DDE), Madurai Kamaraj University, Madurai - 21, Tamil Nadu, India.
authors.forename: Jayavel
authors.initials: J
authors.lastname: Sridhar
authors.affiliation: Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Madurai - 21, Tamil Nadu, India.
authors.forename: Mohan
authors.initials: M
authors.lastname: Pandi
keywords: 4SALE; Endophytes; ITS; MEGA 5.1; ProfDistS; Sequence-secondary structure
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