phylogeny of Turnip mosaic virus; comparisons of 38 genomic sequences reveal a Eurasian origin and a recent 'emergence' in east Asia

The genomes of a representative world‐wide collection of 32 Turnip mosaic virus (TuMV) isolates were sequenced and these, together with six previously reported sequences, were analysed. At least one‐fifth of the sequences were recombinant. In phylogenetic analyses, using genomic sequences of Japanese yam mosaic virus as an outgroup, the TuMV sequences that did not show clear recombination formed a monophyletic group with four well‐supported lineages. These groupings correlated with differences in pathogenicity and provenance; the sister group to all others was of Eurasian B‐strain isolates from nonbrassicas, and probably represents the ancestral TuMV population, and the most recently ‘emerged’ branch of the population was probably that of the BR‐strain isolates found only in east Asia. Eight isolates, all from east Asia, were clear recombinants, probably the progeny of recent recombination events, whereas a similar number, from other parts of the world, were seemingly older recombinants. This difference indicates that the presence of clear recombinants in a subpopulation may be a molecular signature of a recent ‘emergence’.