African Journal of
Microbiology Research

  • Abbreviation: Afr. J. Microbiol. Res.
  • Language: English
  • ISSN: 1996-0808
  • DOI: 10.5897/AJMR
  • Start Year: 2007
  • Published Articles: 5230

Full Length Research Paper

Insights on genetic diversity and phylogenetic analysis of Hop stunt viroid (HSVd) population from symptomatic citrus tree in Tunisia

Hamdi I.1,  Elleuch A.3, Bessaies N.2, Fakhfakh H.1*
  1Laboratoire de Génétique moléculaire, Immunologie et Biotechnologie, Faculté des Sciences de Tunis, Campus Universitaire El Manar, 2092, Tunis, Tunisie. 2Centre technique d es agrumes, 2010, La Manouba, Ministère de l’agriculture de Tunis. 3Faculté des Sciences de Sfax, Laboratoire de biotechnologie Appliquée à l’amélioration des cultures, Tunisie.
Email: [email protected]

  •  Accepted: 13 September 2011
  •  Published: 09 October 2011

Abstract

 

Hop stunt viroid (HSVd) variants from cachexia symptomatic citrus tree were subjected to retro-transcription and DNA amplification (RT-PCR), cloning and sequencing. Here we report genetic diversity and phylogenetic analysis of HSVd Tunisian isolate. Our study revealed obvious polymorphism within Tunisian isolates and high similarity with Japanese variants. Neighbor-joining analysis was carried out on the new HSVd-citrus sequences together with 44 previously described HSVd isolates from citrus and one from grapevine. The phylogenetic analysis showed that Tunisian isolates were clustered into 4 different groups (CVd-IIa, b, and c and grapevine group). Furthermore, the predicted secondarystructure was scrutinized to be more understanding on how the nucleotide change affects variable (V) and pathogenicity domain (P).

 

Key words: Hop stunt viroid (HSVd), citrus, cachexia, phylogeny, secondary structure, Tunisia