Molecular characterization of an almond isolate of Prune dwarf virus in Tunisia: putative recombination breakpoints in the partial sequences of the coat protein-encoding gene in isolates from different geographic origin

Recombination is an important driving force in evolution. To investigate this evolutionary process in Prune dwarf virus (PDV), 31 accessions retrieved from international databases, supplemented by one Tunisian isolate described here, were analyzed. Two recombination detection programs were used: RDP v3.31 beta and RECCO. While the first program did not detect any significant recombination events, RECCO detected several breakpoints in partial sequences of the coat protein gene (CP) of fifteen isolates. The Tajima neutrality test implemented in the MEGA4.1 beta program indicated that there were numerous deletion/insertion events in the sequences. The strongest signal was found in Portuguese isolate 3.12N.14 (accession number AY646846) which had position nt 296-523 in the CP gene. The evolutionary historical relationships between all analyzed isolates were determined by constructing a dendrogram using Neighbor joining (NJ), Minimum evolution (ME), Maximum parsimony (MP), Maximum likelihood (ML), and the Unweighted pair group method with arithmetic mean (UPGMA); all gave similar results. Two main clusters were delineated, one representing recombinant and one nonrecombinant isolates. The recombinant isolates were mostly collected from Portugal, whereas the nonrecombinant isolates originated in eastern Europe.