title: Evaluation of the genetic diversity of Plum pox virus in a single plum tree.
abstract: Genetic diversity of Plum pox virus (PPV) and its distribution within a single perennial woody host (plum, Prunus domestica) has been evaluated. A plum tree was triply infected by chip-budding with PPV-M, PPV-D and PPV-Rec isolates in 2003 and left to develop untreated under open field conditions. In September 2010 leaf and fruit samples were collected from different parts of the tree canopy. A 745-bp NIb-CP fragment of PPV genome, containing the hypervariable region encoding the CP N-terminal end was amplified by RT-PCR from each sample and directly sequenced to determine the dominant sequence. In parallel, the PCR products were cloned and a total of 105 individual clones were sequenced. Sequence analysis revealed that after 7 years of infection, only PPV-M was still detectable in the tree and that the two other isolates (PPV-Rec and PPV-D) had been displaced. Despite the fact that the analysis targeted a relatively short portion of the genome, a substantial amount of intra-isolate variability was observed for PPV-M. A total of 51 different haplotypes could be identified from the 105 individual sequences, two of which were largely dominant. However, no clear-cut structuration of the viral population by the tree architecture could be highlighted although the results obtained suggest the possibility of intra-leaf/fruit differentiation of the viral population. Comparison of the consensus sequence with the original source isolate showed no difference, suggesting within-plant stability of this original isolate under open field conditions.
authors.affiliation: Institute of Virology, Department of Plant Virology, Slovak Academy of Sciences, Dúbravská cesta 9, 84505 Bratislava, Slovakia.
authors.forename: Lukáš
authors.initials: L
authors.lastname: Predajňa
authors.forename: Zdeno
authors.initials: Z
authors.lastname: Šubr
authors.forename: Thierry
authors.initials: T
authors.lastname: Candresse
authors.forename: Miroslav
authors.initials: M
authors.lastname: Glasa
mesh_terms: D014644:Genetic Variation; D008969:Molecular Sequence Data; D010802:Phylogeny; D010935:Plant Diseases / Q000821:virology*; D017801:Plum Pox Virus / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification*; D027861:Prunus / Q000821:virology*