The temporal evolution and global spread of Cauliflower mosaic virus, a plant pararetrovirus.
Cauliflower mosaic virus (CaMV) is a plant pararetrovirus with a double-stranded DNA genome. It is the type member of the genus Caulimovirus in the family Caulimoviridae. CaMV is transmitted by sap inoculation and in nature by aphids in a semi-persistent manner. To investigate the patterns and timescale of CaMV migration and evolution, we sequenced and analyzed the genomes of 67 isolates of CaMV collected mostly in Greece, Iran, Turkey, and Japan together with nine published sequences. We identified the open-reading frames (ORFs) in the genomes and inferred their phylogeny. After removing recombinant sequences, we estimated the substitution rates, divergence times, and phylogeographic patterns of the virus populations. We found that recombination has been a common feature of CaMV evolution, and that ORFs I-V have a different evolutionary history from ORF VI. The ORFs have evolved at rates between 1.71 and 5.81×10(-4) substitutions/site/year, similar to those of viruses with RNA or ssDNA genomes. We found four geographically confined lineages. CaMV probably spread from a single population to other parts of the world around 400-500 years ago, and is now widely distributed among Eurasian countries. Our results revealed evidence of frequent gene flow between populations in Turkey and those of its neighboring countries, with similar patterns observed for Japan and the USA. Our study represents the first report on the spatial and temporal spread of a plant pararetrovirus.
Laboratory of Plant Virology, Faculty of Agriculture, Saga University, Saga, Japan.
Ryosuke
R
Yasaka
Laboratory of Plant Virology, Faculty of Agriculture, Saga University, Saga, Japan ; The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan.
Huy D
HD
Nguyen
School of Biological Sciences, University of Sydney, Sydney, New South Wales, Australia.
Simon Y W
SY
Ho
School of Biological Sciences, University of Sydney, Sydney, New South Wales, Australia.
Sebastián
S
Duchêne
Department of Plant Protection, Faculty of Agriculture, University of Canakkale Onsekiz Mart, Canakkale, Turkey.
Savas
S
Korkmaz
Plant Pathology Laboratory, Faculty of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, Greece.
Nikolaos
N
Katis
Graduate School of Agricultural Science, Faculty of Agriculture, Tohoku University, Sendai, Japan.
Hideki
H
Takahashi
Emeritus Faculty, Australian National University, Canberra, Australia.
Adrian J
AJ
Gibbs
Laboratory of Plant Virology, Faculty of Agriculture, Saga University, Saga, Japan ; The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan.
Kazusato
K
Ohshima
D000818:Animals; D001042:Aphids / Q000821:virology; D005075:Biological Evolution; D001937:Brassica / Q000821:virology; D017796:Caulimovirus / Q000145:classification / Q000235:genetics*; D004279:DNA, Viral / Q000235:genetics*; D016679:Genome, Viral; D007303:Insect Vectors / Q000821:virology; D007564:Japan; D019083:Mediterranean Region; D016366:Open Reading Frames; D010802:Phylogeny; D058974:Phylogeography; D010935:Plant Diseases / Q000821:virology; D062211:Spatio-Temporal Analysis
D004279:DNA, Viral