ISSN 2736-1756
Advanced Journal of Microbiology Research ISSN 2241-9837 Vol. 13 (5), pp. 001-011, May, 2019. © International Scholars Journals
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 and 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.
Accepted 13 March, 2019
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 secondary structure 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.