Temporal analysis of reassortment and molecular evolution of Cucumber mosaic virus: Extra clues from its segmented genome

- Present-day CMV lineages had a most recent common ancestor 1550-2600 years ago.
- The CMV population mostly radiated less than 295-545 years ago.
- No reassortant found in the present populations is more than 251 years old.
- The open-reading frames evolve at around 2.3-4.7×10−4 substitutions/site/year.
- Synonymous codons of CMV seem to have a more precise temporal signal than all codons.

Cucumber mosaic virus (CMV) is a damaging pathogen of over 200 mono- and dicotyledonous crop species worldwide. It has the broadest known host range of any virus, but the timescale of its evolution is unknown. To investigate the evolutionary history of this virus, we obtained the genomic sequences of 40 CMV isolates from brassicas sampled in Iran, Turkey and Japan, and combined them with published sequences. Our synonymous ('silent') site analyses revealed that the present CMV population is the progeny of a single ancestor existing 1550-2600 years ago, but that the population mostly radiated 295-545 years ago. We found that the major CMV lineages are not phylogeographically confined, but that recombination and reassortment is restricted to local populations and that no reassortant lineage is more than 251 years old. Our results highlight the different evolutionary patterns seen among viral pathogens of brassica crops across the world.