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

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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.

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Acknowledgments

This study was supported by the Ministry of Higher Education and Scientific Research of Tunisia and partially by a Franco-Tunisian Utique program (PHC-Utique 10G0905). We acknowledge the help of the Tunisian Ministry of Agriculture with surveys.

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Authors and Affiliations

  1. Laboratory of Molecular Genetics, Immunology and Biotechnology, Faculty of Sciences, University of Tunis El Manar, Tunis, Tunisia

    Charfeddine Gharsallah, Amina Ben Halima, Hatem Fakhfakh & Faten Gorsane

  2. Faculty of Sciences of Bizerte, University of Carthage, 7021, Zarzouna, Tunisia

    Hatem Fakhfakh & Faten Gorsane

Authors
  1. Charfeddine Gharsallah
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  2. Amina Ben Halima
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  3. Hatem Fakhfakh
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  4. Faten Gorsane
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Correspondence to Faten Gorsane.

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Gharsallah, C., Halima, A.B., Fakhfakh, H. et al. Insights into the genetic diversity and the phylogenetic analysis of Tunisian isolates of Tomato chlorosis virus . Phytoparasitica 43, 87–96 (2015). https://doi.org/10.1007/s12600-014-0423-4

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  • DOI: https://doi.org/10.1007/s12600-014-0423-4

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