Evaluating Short Sequence Repeats (SSRs) Markers in Sordaria fimicola by High Resolution Melt Analysis

Abstract

Sordaria fimicola is found worldwide but little is known about its population structure in any region. To bridge this knowledge gap, we attempted to develop molecular markers to study the genetic variations and population structure in the natural strains of S. fimicola. Based on the whole genome sequence of S. macrospora we targeted sixteen genomic regions that contain short sequence repeats (SSRs). Primers were then designed to amplify the homologous regions in S. fimicola. We used high resolution melt (HRM) analyses and amplicon sequencing to analyse the genetic diversity of the wild strains of S. fimicola collected from the opposing slopes (i.e., South facing slope and North facing slope) of the Evolution Canyon (EC), representing contrasting environments. We found twelve regions that were homologous to that of S. macrospora containing (CAT)7, (TTG)7, (T)14, (GAA)7, (CGT)6, (AAGCAC)6, (GT)5, (GGC)6 (ACA)8, (CTG)7 (CT)6 and (CAGGGG)5 were first time reported in S. fimicola. During this genotyping of SSRs we found variations in SSRs motif number and enrichment in strains isolated from stressed and harsh environment than strains from natural and benign environment in Evolution Canyon. The findings favour the hypothesis that genetic variations are present in strains of stressed environment.

Genetic Variation and Its Reflection on Posttranslational Modifications in Frequency Clock and Mating Type a-1 Proteins inSordaria fimicola

“…Thorough literature study does suggest that this is the first attempt to explore the genetic diversity of S. fimicola in natural populations of Evolution Canyon using SSR markers. Arif et al [ 38 ] targeted 16 regions from S. macrospora containing short sequence repeats to genotype these SSRs flanking region in different natural strains of S. fimicola and found 12 homologous regions similar to that of S. macrospora . They found high enrichment of SSRs motif and variation in motifs number in strains isolated from south facing slope of EC as compared to strains from north facing slope of EC.…”

Protease production and molecular characterization of a protease dipeptidyl-aminopeptidase gene from different strains of Sordaria fimicola

“…The polymorphism can also be observed in the specific gene regions of nucleotide sequences within species and closely related organisms (Park et al, 2007). Same strategies to predict PTMs of histone 3 and 4 protein, manganese oxide super disumtase protein were adopted (Jawaria et al, 2018;Jamil et al, 2018). Nuclear export possesses several pathways (Ossareh-Nazari et al, 2001).…”