Evolutionary trajectory of turnip mosaic virus populations adapting to a new host.

Little is known about how some plant viruses establish successful cross-species transmission whilst others do not; the genetic basis for adaptation is largely unknown. This study investigated the genetic changes that occurred using the progeny of an infectious clone, p35Tunos, derived from the turnip mosaic virus (TuMV) UK 1 isolate, which has a Brassica host type, but rarely infects Raphanus systemically and then only asymptomatically. The genetic trajectory leading to viral adaptation was studied in a TuMV isolate passaged in Nicotiana benthamiana (parental), Brassica rapa, the old (susceptible) host and Raphanus sativus, the new (almost insusceptible) host. Almost-complete consensus genomic sequences were obtained by RT-PCR of viral populations passaged up to 35 times together with 59 full sequences of 578,200 nt. There were significant differences in the nucleotide and encoded amino acid changes in the consensus genomes from the old and new hosts. Furthermore, a 3264 nt region corresponding to nt 3222-6485 of the UK 1 genome was cloned, and 269 clones from 23 populations were sequenced; this region covered 33 % of the genome and represented a total of 878,016 nt. The results showed that the nucleotide diversity and the non-synonymous/synonymous ratio of the populations from the new host were higher than those from the old host. An analysis of molecular variance showed significant differences among the populations from the old and new hosts. As far as is known, this is the first report comparing the evolutionary trajectory dynamics of plant virus populations in old and new hosts.

Patterns of recombination in turnip mosaic virus genomic sequences indicate hotspots of recombination.

Potyviruses have variable single-stranded RNA genomes and many show clear evidence of recombination. This report studied the distribution of recombination sites in the genomes of 92 isolates of the potyvirus Turnip mosaic virus (TuMV); 42 came from the international gene sequence databases and an additional 50 complete genomic sequences were generated from field samples collected in Europe and Asia. The sequences were examined for evidence of recombination using seven different sequence comparison methods and the exact position of each site was confirmed by sequence composition analysis. Recombination sites were found throughout the genomes, except in the small 6K1 protein gene, and only 24 of the genomes (26%) showed no evidence of recombination. Statistically significant clusters of recombination sites were found in the P1 gene and in the CI/6K2/VPg gene region. Most recombination sites were bordered by an upstream (5') region of GC-rich and downstream (3') region of AU-rich sequence of a similar length. Correlations between the presence and type of recombination site and provenance, host type and phylogenetic relationships are discussed, as is the role of recombination in TuMV evolution.