Complete nucleotide sequence of the geonomic RNA of a mild strain of Japanese yam mosaic potyvirus

Fuji, Shin-ichi; Nakamae, H.

doi:10.1007/s007050050052

Cited by 25 publications

(14 citation statements)

References 14 publications

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“…Analyses of the phylogenetic relationships were confined to the 30 sequences that did not show clear evidence of recombination, the nonrecombinant TuMV sequences. The homologous regions of the genomes of two isolates (J1 and Mild) of JYMV (Fuji & Nakamae 1999, 2000) were used as the outgroup for these analyses as blast searches had shown them to be the sequences in the international sequence databases most closely and consistently related to those of TuMV; their nucleotide sequences differed from those of TuMV by ≈ 15%; ranging from 10% to 23% in different parts of the genome. The genomic sequence of Scallion mosaic virus (Chen et al .…”

Section: Resultsmentioning

confidence: 99%

The phylogeny ofTurnip mosaic virus; comparisons of 38 genomic sequences reveal a Eurasian origin and a recent ‘emergence’ in east Asia

Tomimura

Gibbs

Jenner³

et al. 2003

Molecular Ecology

115

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The genomes of a representative world-wide collection of 32 Turnip mosaic virus (TuMV) isolates were sequenced and these, together with six previously reported sequences, were analysed. At least one-fifth of the sequences were recombinant. In phylogenetic analyses, using genomic sequences of Japanese yam mosaic virus as an outgroup, the TuMV sequences that did not show clear recombination formed a monophyletic group with four well-supported lineages. These groupings correlated with differences in pathogenicity and provenance; the sister group to all others was of Eurasian B-strain isolates from nonbrassicas, and probably represents the ancestral TuMV population, and the most recently 'emerged' branch of the population was probably that of the BR-strain isolates found only in east Asia. Eight isolates, all from east Asia, were clear recombinants, probably the progeny of recent recombination events, whereas a similar number, from other parts of the world, were seemingly older recombinants. This difference indicates that the presence of clear recombinants in a subpopulation may be a molecular signature of a recent 'emergence'.

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Section: Resultsmentioning

confidence: 99%

The phylogeny ofTurnip mosaic virus; comparisons of 38 genomic sequences reveal a Eurasian origin and a recent ‘emergence’ in east Asia

Tomimura

Gibbs

Jenner³

et al. 2003

Molecular Ecology

115

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“…Two genomic sequences of JYMV [10], [11], one of ScMV [12], and one of NYSV [13] were used as outgroups because BLAST searches had shown them to be most closely and consistently related to those of TuMV. TuMV Protein 1 (P1) genes were more closely related to those of JYMV than to those of ScMV, whereas for some intergenic regions between helper component-proteinase protein (HC-Pro) and nuclear inclusion b protein (NIb) the converse was true.…”

Section: Methodsmentioning

confidence: 99%

“…One of these is the ‘TuMV group’, which comprises TuMV and at least five other species, all from monocotyledonous plants. These include Japanese yam mosaic virus (JYMV) [10], [11], Narcissus yellow stripe virus (NYSV) [12], and Scallion mosaic virus (ScMV) [13], all known from full genomic sequences. Sequence analyses of the coat protein have shown that the TuMV group also contains Indian narcissus potyvirus and Narcissus late season yellows potyvirus.…”

Section: Introductionmentioning

confidence: 99%

Turnip Mosaic Potyvirus Probably First Spread to Eurasian Brassica Crops from Wild Orchids about 1000 Years Ago

et al. 2013

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Turnip mosaic potyvirus (TuMV) is probably the most widespread and damaging virus that infects cultivated brassicas worldwide. Previous work has indicated that the virus originated in western Eurasia, with all of its closest relatives being viruses of monocotyledonous plants. Here we report that we have identified a sister lineage of TuMV-like potyviruses (TuMV-OM) from European orchids. The isolates of TuMV-OM form a monophyletic sister lineage to the brassica-infecting TuMVs (TuMV-BIs), and are nested within a clade of monocotyledon-infecting viruses. Extensive host-range tests showed that all of the TuMV-OMs are biologically similar to, but distinct from, TuMV-BIs and do not readily infect brassicas. We conclude that it is more likely that TuMV evolved from a TuMV-OM-like ancestor than the reverse. We did Bayesian coalescent analyses using a combination of novel and published sequence data from four TuMV genes [helper component-proteinase protein (HC-Pro), protein 3(P3), nuclear inclusion b protein (NIb), and coat protein (CP)]. Three genes (HC-Pro, P3, and NIb), but not the CP gene, gave results indicating that the TuMV-BI viruses diverged from TuMV-OMs around 1000 years ago. Only 150 years later, the four lineages of the present global population of TuMV-BIs diverged from one another. These dates are congruent with historical records of the spread of agriculture in Western Europe. From about 1200 years ago, there was a warming of the climate, and agriculture and the human population of the region greatly increased. Farming replaced woodlands, fostering viruses and aphid vectors that could invade the crops, which included several brassica cultivars and weeds. Later, starting 500 years ago, inter-continental maritime trade probably spread the TuMV-BIs to the remainder of the world.

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“…The concats were used for evolutionary analyses. The corresponding regions of two sequences of Japanese yam mosaic virus (JYMV) (Fuji & Nakamae 1999, 2000), one of Scallion mosaic virus (ScMV) (Chen et al . 2002) and one of Narcissus yellow stripe virus (NYSV) (Chen et al .…”

Section: Methodsmentioning

confidence: 99%

A phylogeographical study of theTurnip mosaic viruspopulation in East Asia reveals an ‘emergent’ lineage in Japan

Tomitaka

Ohshima

2006

Molecular Ecology

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The genetic structure of populations of Turnip mosaic virus (TuMV) in East Asia was assessed by making host range and gene sequence comparisons of 118 isolates utilizing a population genetic approach. Most, but not all, isolates collected from Brassica plants in China infected only Brassica plants, whereas those from Japan infected both Brassica and Raphanus (BR) plants. Analyses of the positions of recombination sites in five regions of the genomes (one third of the full sequence) of the many recombinant isolates were fully congruent with the results of phylogenetic analysis, and at least one recombination type pattern was shared between Chinese and Japanese populations. One lineage of nonrecombinant isolates from the basal-BR lineage was found in 2000 in Kyushu, Japan but none in China, and have since been found over the whole island. The sudden expansion of this basal-BR population was strongly supported by calculations showing the deviations from the neutral equilibrium model for the individual geographical lineages with overall lack of nucleotide diversity, and by analysis of mismatch distribution. Our study shows that the recent Chinese and Japanese TuMV isolates are part of the same population but are discrete lineages.

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Complete nucleotide sequence of the geonomic RNA of a mild strain of Japanese yam mosaic potyvirus

Cited by 25 publications

References 14 publications

The phylogeny ofTurnip mosaic virus; comparisons of 38 genomic sequences reveal a Eurasian origin and a recent ‘emergence’ in east Asia

The phylogeny ofTurnip mosaic virus; comparisons of 38 genomic sequences reveal a Eurasian origin and a recent ‘emergence’ in east Asia

Turnip Mosaic Potyvirus Probably First Spread to Eurasian Brassica Crops from Wild Orchids about 1000 Years Ago

A phylogeographical study of theTurnip mosaic viruspopulation in East Asia reveals an ‘emergent’ lineage in Japan

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