Phylogenetic Analysis of Rust Causing Fungi Based on Selected Loci of Coding Region

Abstract

n present study rust species from different regions of Pakistan were comparatively screened for beta tubulin and translation elongation factor in order to analyze the phylogeny of Puccinia spp. Beta tubulin and translation elongation factor are the polymorphic sequences of genes, which help in determination of genetic variation. This study revealed that point mutation is the major sequence variation including the heterokaryotic variation within the species and homokaryotic variation among the species. The phylogenetic analysis of these rust species illustrated high similarity with globally distributed varieties present in NCBI. The amplified products were further characterized through nucleotide sequence assay. Multiple sequence alignment revealed significant genetic diversity in rust loci. The protein sequences of beta tubulin and translation elongation factor genes demonstrated 3-D structures and functional helical domains verifying the stability of proteins and showing differences in disordered factor (unstability) and alpha helix (stability). Furthermore, the Protparam and Pepstats (Expasy) demonstrated differences in physiochemical properties of these proteins. Similarly, the molecular weight and isoelectric values pointed to the possible antimicrobial activity. The present study further suggested that the coding regions are more efficient in identification of rust species compared to non-coding regions. As the coding regions are conserved regions with least error rate and these conserved regions play a vital role in phylogenetic analysis. In future, advance computational assay will help to identify the mutational sites in these species and will assist to overcome rust associated problems in the field of agriculture.