Evaluating short sequence repeats (SSRs) markers in Sordaria fimicola by high resolution melt analysis

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.