Inter- and intralineage recombinants are common in natural populations of Turnip mosaic virus

1 Laboratory of Plant Virology, Faculty of Agriculture, Saga University, Saga 840-8502, Japan 2 Laboratory of Animal Production and Management, Faculty of Agriculture, Saga University, Saga 840-8502, Japan 3 BioInfomatics Research Division, Japan Science and Technology Corporation, Tokyo 102-0081, Japan 4 Institute of Bioengineering, Zhejiang University of Science and Technology, Hangzhou Xiasha 310018, PR China Correspondence Kazusato Ohshima ohshimak{at}cc.saga-u.ac.jp A recombination map of the genome of Turnip mosaic virus (TuMV) was assembled using data from 19 complete genomic sequences, previously reported, and a composite sample of three regions of the genome, one-third in total, of a representative Asia-wide collection of 70 isolates. Thus, a total of 89 isolates of worldwide origin was analysed for recombinants. Eighteen recombination sites were found spaced throughout the 5' two-thirds of the genome, but there were only two in the 3' one-third; thus, 24 and 35 % of the P1 and NIa-VPg gene sequences examined were recombinants, whereas only 1 % of the corresponding NIa-Pro and CP gene sequences were recombinants. Recombinants with parents from the same or from different lineages were found, and some recombination sites characterized particular lineages. Most of the strain BR recombinants belonged to the Asian-BR group, as defined previously, and it was concluded that this lineage resulted from a recent migration, whereas many of the strain B recombinants from Asia fell into the world-B group. Again, a large proportion of isolates in this group were recombinants. Some recombination sites were found only in particular lineages, and hence seemed more likely to be the surviving progeny from single recombinational events, rather than the progeny of multiple events occurring at recombination hotspots. It seems that the presence of recombination sites, as well as sequence similarities, may be used to trace the migration and evolution of TuMV. The GenBank/EMBL/DDBJ accession numbers of the nucleotide sequence data obtained in this study are AB179888 – AB180040 .