title: Molecular evolution of Turnip mosaic virus: evidence of host adaptation, genetic recombination and geographical spread.
abstract: Turnip mosaic virus (TuMV), a species of the genus Potyvirus, occurs worldwide. Seventy-six isolates of TuMV were collected from around the world, mostly from Brassica and Raphanus crops, but also from several non-brassica species. Host tests grouped the isolates into one or other of two pathotypes; Brassica (B) and Brassica-Raphanus (BR). The nucleotide sequences of the first protein (P1) and coat protein (CP) genes of the isolates were determined. One-tenth of the isolates were found to have anomalous and variable phylogenetic relationships as a result of recombination. The 5'-terminal 300 nt of the P1 gene of many isolates was also variable and phylogenetically anomalous, whereas the 380 nt 3' terminus of the CP gene was mostly conserved. Trees calculated from the remaining informative parts of the two genes of the non-recombinant sequences by neighbour-joining, maximum-likelihood and maximum-parsimony methods were closely similar, and so these parts of the sequences were concatenated and trees calculated from the resulting 1150 nt. The isolates fell into four consistent groups; only the relationships of these groups with one another and with the outgroup differed. The "basal-B" cluster of eight B-pathotype isolates was most variable, was not monophyletic, and came from both brassicas and non-brassicas from southwest and central Eurasia. Closest to it, and forming a monophyletic subgroup of it in most trees, and similarly variable, was the "basal-BR" group of eight BR pathotype Eurasian isolates. The third and least variable group, the "Asian-BR" group, was of 22 BR-pathotype isolates, all from brassicas, mostly Raphanus, and all from east Asia mostly Japan. The fourth group of 36 isolates, the "world-B" group, was from all continents, most were isolated from brassicas and most were of the B-pathotype. The simplest of several possible interpretations of the trees is that TuMV originated, like its brassica hosts, in Europe and spread to the other parts of the world, and that the BR pathotype has recently evolved in east Asia.
authors.affiliation: Laboratory of Plant Virology, Faculty of Agriculture, Saga University, Saga 840-8502, Japan1.
authors.forename: Kazusato
authors.initials: K
authors.lastname: Ohshima
authors.affiliation: Laboratory of Plant Virology, Faculty of Agriculture, Saga University, Saga 840-8502, Japan1.
authors.forename: Yuka
authors.initials: Y
authors.lastname: Yamaguchi
authors.affiliation: Laboratory of Plant Virology, Faculty of Agriculture, Saga University, Saga 840-8502, Japan1.
authors.forename: Ryo
authors.initials: R
authors.lastname: Hirota
authors.affiliation: Laboratory of Plant Virology, Faculty of Agriculture, Saga University, Saga 840-8502, Japan1.
authors.forename: Tamaki
authors.initials: T
authors.lastname: Hamamoto
authors.affiliation: Laboratory of Plant Virology, Faculty of Agriculture, Saga University, Saga 840-8502, Japan1.
authors.forename: Kenta
authors.initials: K
authors.lastname: Tomimura
authors.affiliation: Laboratory of Plant Virology, Faculty of Agriculture, Saga University, Saga 840-8502, Japan1.
authors.forename: Zhongyang
authors.initials: Z
authors.lastname: Tan
authors.affiliation: Laboratory of Plant Pathology, Faculty of Agriculture & Life Sciences, Hirosaki University, Hirosaki 036-8561, Japan2.
authors.forename: Teruo
authors.initials: T
authors.lastname: Sano
authors.affiliation: Tohoku Seed Co. Ltd, Utsunomiya 321-3232, Japan3.
authors.forename: Fumio
authors.initials: F
authors.lastname: Azuhata
authors.affiliation: Plant Pathology & Microbiology Department, Horticulture Research International, Wellesbourne, Warwick CV35 9EF, UK4.
authors.forename: John A
authors.initials: JA
authors.lastname: Walsh
authors.affiliation: Crop & Food Research, Private Bag 4704, Christchurch, New Zealand5.
authors.forename: John
authors.initials: J
authors.lastname: Fletcher
authors.affiliation: Faculty of Life Science, Zhenjiang University, Hangzhou 310029, PR China6.
authors.forename: Jishuang
authors.initials: J
authors.lastname: Chen
authors.affiliation: Department of Virology, Agriculture Research Organization, The Volcani Centre, Bet Dagan 50250, Israel7.
authors.forename: Abed
authors.initials: A
authors.lastname: Gera
authors.affiliation: Faculty of Science, Australian National University, Canberra, ACT 2601, Australia8.
authors.forename: Adrian
authors.initials: A
authors.lastname: Gibbs
mesh_terms: D020413:3' Untranslated Regions / Q000235:genetics; D020121:5' Untranslated Regions / Q000235:genetics; D001208:Asia; D001937:Brassica / Q000821:virology; D019607:Brassicaceae / Q000821:virology*; D005060:Europe; D019143:Evolution, Molecular; D008969:Molecular Sequence Data; D010802:Phylogeny; D017800:Potyvirus / Q000145:classification* / Q000235:genetics; D011995:Recombination, Genetic; D014764:Viral Proteins / Q000235:genetics
chemical_list: D020413:3' Untranslated Regions; D020121:5' Untranslated Regions; D014764:Viral Proteins