Molecular phylogeny of geminivirus infecting wild plants in Japan

Few studies have been made on the molecular divergence of plant viruses. To remedy this deficiency, we examined the molecular divergence of the tobacco leaf curl geminivirus (TLCV). TLCV infects not only tobacco but also Eupatorium and Lonicera in the field and causes yellow vein disease. A total of 29 nucleotide sequences of the replication protein gene (ORF C1) of geminiviruses infecting wild plants of E. makinoi, E. glehni and L. japonica collected from ten localities was determined. Highly divergent sequences were obtained not only among host plant populations but also within a host population. Phylogenetic analyses showed that the TLCVs infecting Eupatorium and Lonicera were clustered into three different clades, and were either paraphyletic or polyphyletic. This result is the first evidence demonstrating that wild populations of single plant species possess genetically diversified virus strains. Comparison with recently reported genetic variations of tobacco mild green mosaic tobamovirus (TMGMV) revealed three characteristics of TLCV evolution: (1) a higher nucleotide substitution rate, (2) more frequent migration among geographically isolated host populations, and (3) more frequent host changes to different plant families. While TMGMV is an RNA virus, TLCV has DNA genomes. In animal viruses, RNA viruses tend to evolve faster than DNA viruses. Our results indicated that this trend may not hold for plant viruses.