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
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