Insights into the genetic diversity and the phylogenetic analysis of Tunisian isolates of Tomato chlorosis virus

Abstract

A one-step RT-PCR was used to identify Tomato chlorosis virus (ToCV) (Crinivirus members) infections on some Tunisian cultures. Results provided evidence that the ToCV is the most prevalent virus on Tunisian tomato crops. Findings were validated with specific primers. Genetic analysis of ToCV isolates was explored based on sequence data of viral segments within the coat protein (CP), the heat shock protein (HSP70h) and the polymerase protein (RdRp). Synonymous (dS) and non-synonymous (dN) substitution rates and their ratio were analyzed. The patterns of mutations were shaped depending on the considered fragment from the three viral regions. Selective neutrality test was significantly negative, suggesting a recent expansion of ToCV isolates. Pairwise mismatch distribution gave a bimodal pattern and pointed to the clustering of ToCV isolates into two distinct geographical clades. Genetic haplotype network provided evidence of the existence of two distinct clusters. The star-like shaped pattern confirmed recent expansion of ToCV isolates.