@article{fdi:010088953,
  title = {{R}evisiting the origins of the {S}obemovirus genus : a case for ancient origins of plant viruses},
  author = {{G}hafari, {M}. and {S}omera, {M}. and {S}armiento, {C}. and {N}iehl, {A}. and {H}{\'e}brard, {E}ug{\'e}nie and {T}soleridis, {T}. and {B}all, {J}. and {M}oury, {B}. and {L}emey, {P}. and {K}atzourakis, {A}. and {F}argette, {D}enis},
  editor = {},
  language = {{ENG}},
  abstract = {{T}he discrepancy between short- and long-term rate estimates, known as the time-dependent rate phenomenon ({TDRP}), poses a challenge to extrapolating evolutionary rates over time and reconstructing evolutionary history of viruses. {T}he {TDRP} reveals a decline in evolutionary rate estimates with the measurement timescale, explained empirically by a power-law rate decay, notably observed in animal and human viruses. {A} mechanistic evolutionary model, the {P}risoner of {W}ar ({P}o{W}) model, has been proposed to address {TDRP} in viruses. {A}lthough {TDRP} has been studied in animal viruses, its impact on plant virus evolutionary history remains largely unexplored. {H}ere, we investigated the consequences of {TDRP} in plant viruses by applying the {P}o{W} model to reconstruct the evolutionary history of sobemoviruses, plant pathogens with significant importance due to their impact on agriculture and plant health. {O}ur analysis showed that the {S}obemovirus genus dates back over four million years, indicating an ancient origin. {W}e found evidence that supports deep host jumps to {P}oaceae, {F}abaceae, and {S}olanaceae occurring between tens to hundreds of thousand years ago, followed by specialization. {R}emarkably, the {TDRP}-corrected evolutionary history of sobemoviruses was extended far beyond previous estimates that had suggested their emergence nearly 9,000 years ago, a time coinciding with the {N}eolithic period in the {N}ear {E}ast. {B}y incorporating sequences collected through metagenomic analyses, the resulting phylogenetic tree showcases increased genetic diversity, reflecting a deep history of sobemovirus species. {W}e identified major radiation events beginning between 4,600 to 2,000 years ago, which aligns with the {N}eolithic period in various regions, suggesting a period of rapid diversification from then to the present. {O}ur findings make a case for the possibility of deep evolutionary origins of plant viruses.},
  keywords = {},
  booktitle = {},
  journal = {{PL}o{S} {P}athogens},
  volume = {20},
  numero = {1},
  pages = {e1011911 [17 p.]},
  ISSN = {1553-7366},
  year = {2024},
  DOI = {10.1371/journal.ppat.1011911},
  URL = {https://www.documentation.ird.fr/hor/fdi:010088953},
}