Phylogenetic and Secondary Structure analysis of rice false smut (Ustilaginoidea virens) fungal isolates using internal transcribed spacer ITS1, 5.8S and ITS2

Abstract

False smut of rice is a fungal disease which converts florets in to yellow colored smut balls, once it was considered as minor disease, has of now it become a serious pathogen in almost all rice growing areas in the world. The disease incidence has been reported at many places in an alarming proportion. However, ambiguity in morphotyping of destructive pathogen which are of quarantine importance is impacted by a number of factors that negatively affect identification. Secondary structural information of the rRNA may be considered to be a conserved region which can be used as supplementary information for possible fungal identification. In the present study the known (four) and query sequences from NCBI (21) were subjected to sequence analyses for their ITS regions. Significant variation was observed for hairpins loops, exterior loop, interior loop, multi loop and bulged loops in all the sequences under investigation.