Complete genomic sequence analyses of Turnip mosaic virus basal-BR isolates from China

Wang, Hongyan; Liu, Jinliang; Gao, Rui; Chen, Jia; Shao, Y.-H.; Li, Xiangdong

doi:10.1007/s11262-009-0335-4

Cited by 19 publications

(25 citation statements)

References 50 publications

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“…None of the samples were from ‘endangered’ species. Details of the isolates are shown in Table S1, together with those of the isolates used in the sequence analyses and for which the complete genomic sequences have already been reported [4], [6], [19]–[30]; GenBank Accession Codes (AF394601, AF394602, and EF374098). The orchid-infecting TuMV-like viruses were isolated from Orchis militaris, Orchis morio , and Orchis simia plants growing in a collection at Celle, Germany.…”

Section: Methodsmentioning

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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Section: Methodsmentioning

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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“…However, isolates from the Australian continent rarely feature in them (e.g. Tomimura et al, 2003;Ohshima et al, 2007;Farzadfar et al, 2009;Wang et al, 2009;Nguyen et al, 2013b). Much of the TuMV literature in recent times has focused on the commonly recombinant nature of TuMV and the evolution of the virus.…”

Section: Introductionmentioning

confidence: 99%

Biological and molecular variation amongst Australian Turnip mosaic virus isolates

et al. 2015

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Turnip mosaic virus (TuMV) causes crop losses worldwide. Eight Australian TuMV isolates originally obtained from five different species in two plant families were inoculated to 14 plant species belonging to four families to compare their host reactions. They differed considerably in virulence in Brassicaceae crop species and virus indicator hosts belonging to three other families. The isolates infected most Brassica species inoculated, but not Raphanus sativus, usually causing systemic mosaic symptoms, so they resembled TuMV biological host type [B]. Whole genome sequences of seven of the Australian isolates were obtained and had lengths of 9834 nucleotides (nt). When they were compared with 37 non-recombinant TuMV genomes from other continents and another whole genome from Australia, six of them formed an Australian group within the overall world-B phylogenetic grouping, while the remaining new genome sequence and the additional whole genome from Australia were part of the basal-B grouping. When the seven new Australian genomes and the additional whole genome from Australia were subjected to recombination analysis, six different recombination events were found. Six genomes contained one or two recombination events each, but one was non-recombinant. The non-recombinant isolate was in the Australian grouping within the overall world-B group while the remaining recombinant isolates were in the basal-B and world-B phylogenetic groups.

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“…TuMV has flexuous filamental particles of 700–750 nm long and can be transmitted by 40–50 species of aphids in a non-persistent manner [ 4 , 5 ]. The TuMV genome consists of one single-stranded positive sense RNA molecule of approximately 9830 nucleotides (nt) and contains a large open reading frame (ORF) [ 6 ]. The genomic RNA is translated into a large polyprotein and a frame-shift protein.…”

Section: Introductionmentioning

confidence: 99%

“…As in other potyviruses [ 19 ], recombination is a frequent event in the evolution of TuMV. Intra- and inter-lineage recombinants are common in natural populations of TuMV and can be detected throughout the genome [ 6 , 20 – 22 ]. The Chinese and Japanese TuMV isolates are part of the same population but are a discrete lineage [ 22 , 23 ].…”

Section: Introductionmentioning

confidence: 99%

The genetic structure of Turnip mosaic virus population reveals the rapid expansion of a new emergent lineage in China

Zhu

Yin

et al. 2017

Virol J

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Background Turnip mosaic virus (TuMV) is one of the most widespread and economically important virus infecting both crop and ornamental species of the family Brassicaceae. TuMV isolates can be classified to five phylogenetic lineages, basal-B, basal-BR, Asian-BR, world-B and Orchis.ResultsTo understand the genetic structure of TuMV from radish in China, the 3′-terminal genome of 90 TuMV isolates were determined and analyzed with other available Chinese isolates. The results showed that the Chinese TuMV isolates from radish formed three groups: Asian-BR, basal-BR and world-B. More than half of these isolates (52.54%) were clustered to basal-BR group, and could be further divided into three sub-groups. The TuMV basal-BR isolates in the sub-groups I and II were genetically homologous with Japanese ones, while those in sub-group III formed a distinct lineage. Sub-populations of TuMV basal-BR II and III were new emergent and in a state of expansion. The Chinese TuMV radish populations were under negative selection. Gene flow between TuMV populations from Tai’an, Weifang and Changchun was frequent.ConclusionsThe genetic structure of Turnip mosaic virus population reveals the rapid expansion of a new emergent lineage in China.

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Complete genomic sequence analyses of Turnip mosaic virus basal-BR isolates from China

Cited by 19 publications

References 50 publications

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

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

Biological and molecular variation amongst Australian Turnip mosaic virus isolates

The genetic structure of Turnip mosaic virus population reveals the rapid expansion of a new emergent lineage in China

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