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Background <p>The discovery of a plum tree isolate of plum pox virus (PPV, <i>Potyvirus plumpoxi</i>), done in Eastern Albania in 2011 in the frame of an EU-funded survey, which represents a divergent strain named PPV-An, proved to be original and informative for the unraveling of PPV evolutionary history.</p> Methods <p>Maximum likelihood and Bayesian phylogenetic methods applied on full-length genomes or selected regions analyzed the affinities of the PPV-An with other PPV strains. Potential recombination events were also evaluated. A refined timeline of PPV evolutionary history integrating recombination events, strains migration and ancestral host state is proposed.</p> Results <p>Altogether, the analyses confirm previous hypotheses that PPV-An corresponds to an ancestral, non-recombinant PPV strain. PPV-An likely served as the origin of the PPV-M and T strains through recombination with isolate(s) of the D strain. Molecular clock analyses dated the most recent common ancestor (TMRCA) of PPV at 4546&#xa0;years ago and phylogeny separated the main PPV strains from the cherry-adapted strains around 3100&#xa0;years ago. Meanwhile, the recombination events that gave rise to the M and T strains are estimated to have occurred in the early sixteenth century of the common era (CE).</p> Conclusions <p>The characterization of the PPV-An strain enabled a comprehensive phylogenetic analysis of PPV. PPV-An is confirmed to be the previously unidentified progenitor, which, together with PPV-D led through recombination to the emergence of the currently prevalent and evolutionary successful recombinant strains of European origin (e.g., M, Rec, and T). The low representation of PPV-An in current PPV populations is likely the consequence of a population replacement phenomenon possibly linked to a higher fitness of the recombinant strains deriving from it. These results highlight the PPV-An strain as a key player in PPV evolutionary history and consolidate PPV as one of the promising models to study host-adaptive evolution processes and phylogeography among the most damaging viruses of agricultural systems.</p>

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Bayesian phylogenetic and recombination analyses of plum pox virus provide a refined vision of its evolutionary history

  • 期刊论文

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  • 发表日期：

    2025年10月1日

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  • F. Palmisano,
  • S. Kawakubo,
  • M. Chiumenti,
  • P. Leonetti,
  • V. Pantaleo,
  • T. Candresse,
  • A. Minafra

摘要

Background

The discovery of a plum tree isolate of plum pox virus (PPV, Potyvirus plumpoxi), done in Eastern Albania in 2011 in the frame of an EU-funded survey, which represents a divergent strain named PPV-An, proved to be original and informative for the unraveling of PPV evolutionary history.

Methods

Maximum likelihood and Bayesian phylogenetic methods applied on full-length genomes or selected regions analyzed the affinities of the PPV-An with other PPV strains. Potential recombination events were also evaluated. A refined timeline of PPV evolutionary history integrating recombination events, strains migration and ancestral host state is proposed.

Results

Altogether, the analyses confirm previous hypotheses that PPV-An corresponds to an ancestral, non-recombinant PPV strain. PPV-An likely served as the origin of the PPV-M and T strains through recombination with isolate(s) of the D strain. Molecular clock analyses dated the most recent common ancestor (TMRCA) of PPV at 4546 years ago and phylogeny separated the main PPV strains from the cherry-adapted strains around 3100 years ago. Meanwhile, the recombination events that gave rise to the M and T strains are estimated to have occurred in the early sixteenth century of the common era (CE).

Conclusions

The characterization of the PPV-An strain enabled a comprehensive phylogenetic analysis of PPV. PPV-An is confirmed to be the previously unidentified progenitor, which, together with PPV-D led through recombination to the emergence of the currently prevalent and evolutionary successful recombinant strains of European origin (e.g., M, Rec, and T). The low representation of PPV-An in current PPV populations is likely the consequence of a population replacement phenomenon possibly linked to a higher fitness of the recombinant strains deriving from it. These results highlight the PPV-An strain as a key player in PPV evolutionary history and consolidate PPV as one of the promising models to study host-adaptive evolution processes and phylogeography among the most damaging viruses of agricultural systems.