Sequence Amplicon Analysis of 18S rDNA Variable Regions (V3, V4 and V9) in Natural Strains of Sordaria fimicola and Response to Different Carbohydrates

Abstract

Employing 18S hypervariable regions as molecular markers, we show a sequence analysis of (V3, V4 and V9) hyper-variable regions of the small sub unit (SSU) of different natural strains of the Pyrenomycete, Sordaria fimicola, to examine genetic diversity. Strains were taken from two contrasting environments (Natural and Harsh) from the south facing and north facing slopes of Evolution Canyon, Israel. Sequenced amplicons were introduced to the NCBI database as a query in BLASTN. The query revealed >100% resemblance with the Ascomycota genus Sordaria and the topmost species in this investigation was fimicola. Circular Phylogram showed close relatedness among the strains under study and potential association with the Ascomycetes. This study for the first time reports the variations at the molecular level between strains from two different environments. V3 and V4 regions showed genetic variations at two sites i.e., 212 A (C); 213 G (A) in strains isolated from the stressful environment while V9 showed no polymorphism. Sequences were submitted to NCBI GenBank under the accession numbers; KY001568; KY000838; KY000839 for S3, N5 and N6 strains. 1% cellulose was found effective to enhance the mycelial and perithecial growth.