The genetic structure of populations of Turnip mosaic virus in Kyushu and central Honshu, Japan

Tomitaka, Yasuhiro; Yamashita, T.; Ohshima, Kazusato

doi:10.1007/s10327-007-0003-2

Cited by 18 publications

(18 citation statements)

References 55 publications

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“…Most, but not all, of the European isolates belonging to the world-B group are B host types, for instance UK 1 is of B host type and belongs to the world-B group, and, although many Brassica plants are susceptible to it, it rarely infects Raphanus sativus and then systemically but asymptomatically. Despite growing interest in the molecular evolution of potyviruses (Moreno et al, 2004;Tan et al, 2004;Tomitaka & Ohshima, 2006;Ohshima et al, 2007;Tomitaka et al, 2007;Gibbs et al, 2008a, b;Ogawa et al, 2008;Seo et al, 2009), there have been few attempts to study their adaptive evolution, although this could provide crucial information about the nature of the interaction between host and virus.…”

Section: Introductionmentioning

confidence: 99%

Evolutionary trajectory of turnip mosaic virus populations adapting to a new host

Ohshima

Akaishi

Kajiyama

et al. 2009

Journal of General Virology

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Little is known about how some plant viruses establish successful cross-species transmission whilst others do not; the genetic basis for adaptation is largely unknown. This study investigated the genetic changes that occurred using the progeny of an infectious clone, p35Tunos, derived from the turnip mosaic virus (TuMV) UK 1 isolate, which has a Brassica host type, but rarely infects Raphanus systemically and then only asymptomatically. The genetic trajectory leading to viral adaptation was studied in a TuMV isolate passaged in Nicotiana benthamiana (parental), Brassica rapa, the old (susceptible) host and Raphanus sativus, the new (almost insusceptible) host. Almost-complete consensus genomic sequences were obtained by RT-PCR of viral populations passaged up to 35 times together with 59 full sequences of 578 200 nt. There were significant differences in the nucleotide and encoded amino acid changes in the consensus genomes from the old and new hosts. Furthermore, a 3264 nt region corresponding to nt 3222-6485 of the UK 1 genome was cloned, and 269 clones from 23 populations were sequenced; this region covered 33 % of the genome and represented a total of 878 016 nt. The results showed that the nucleotide diversity and the non-synonymous/synonymous ratio of the populations from the new host were higher than those from the old host. An analysis of molecular variance showed significant differences among the populations from the old and new hosts. As far as is known, this is the first report comparing the evolutionary trajectory dynamics of plant virus populations in old and new hosts.

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Section: Introductionmentioning

confidence: 99%

Evolutionary trajectory of turnip mosaic virus populations adapting to a new host

Ohshima

Akaishi

Kajiyama

et al. 2009

Journal of General Virology

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“…Crops of the Brassicaceae that are most commonly cultivated in Europe are Brassica spp., whereas both Brassica and Raphanus crops are important in Asia Minor and Asian countries (Tomimura et al, 2003;Tomitaka & Ohshima, 2006;Tomitaka et al, 2007). TuMV isolates are of five hostinfecting types.…”

Section: Introductionmentioning

confidence: 99%

Phylodynamic evidence of the migration of turnip mosaic potyvirus from Europe to Australia and New Zealand

Yasaka

Ohba

Schwinghamer

et al. 2015

Journal of General Virology

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Turnip mosaic virus (TuMV) is a potyvirus that is transmitted by aphids and infects a wide range of plant species. We investigated the evolution of this pathogen by collecting 32 isolates of TuMV, mostly from Brassicaceae plants, in Australia and New Zealand. We performed a variety of sequence-based phylogenetic and population genetic analyses of the complete genomic sequences and of three non-recombinogenic regions of those sequences. The substitution rates, divergence times and phylogeographical patterns of the virus populations were estimated. Six inter-and seven intralineage recombination-type patterns were found in the genomes of the Australian and New Zealand isolates, and all were novel. Only one recombination-type pattern has been found in both countries. The Australian and New Zealand populations were genetically different, and were different from the European and Asian populations. Our Bayesian coalescent analyses, based on a combination of novel and published sequence data from three nonrecombinogenic protein-encoding regions, showed that TuMV probably started to migrate from Europe to Australia and New Zealand more than 80 years ago, and that distinct populations arose as a result of evolutionary drivers such as recombination. The basal-B2 subpopulation in Australia and New Zealand seems to be older than those of the world-B2 and -B3 populations. To our knowledge, our study presents the first population genetic analysis of TuMV in Australia and New Zealand. We have shown that the time of migration of TuMV correlates well with the establishment of agriculture and migration of Europeans to these countries.

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“…The RDP, BOOTSCAN, and SISCAN programs were phylogenetic methods, whereas GENECONV, MAXCHI, and CHIMAERA programs were substitution methods, and the PHYLPRO program was a distance comparison method [29]. Only those sequences supported by at least five software or two kinds of methods were regarded as 'clear' recombinants; otherwise, they were called as 'tentative' recombinants [11,17,18]. Nucleotide diversities of different genes were computed separately for nonsynonymous (d NS ) and synonymous (d S ) positions in coat protein-coding regions by using PBL methods [33,34].…”

Section: Sequence Analyses and Recombination Detectionmentioning

confidence: 99%

“…The conserved amino acids FDSS [46] at position 2611-2614 of the polyprotein was located 266 aa upstream of the putative NIb/CP cleavage site. The conserved (S/T)G-(X) 3 -T(X) 3 -N(S/T)(X) [18][19][20][21][22][23][24][25][26][27][28][29][30][31][32][33][34][35][36][37] GDD that is necessary for RNA polymerase activity and NTP binding began at position 2669. In CP, the DAG motif that interacts with PTK of HC-Pro to regulate virus transmission by aphids [47] was located at position 2882-2884.…”

Section: Genome Structure and Characterization Of Putative Polyproteinsmentioning

confidence: 99%

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

et al. 2009

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Isolates of Turnip mosaic virus (TuMV) are divided into four molecular lineages based on host range and geographical origins. Basal-BR is one of the four lineages and represented a new emergent lineage in East Asia. In one previous paper, we report the occurrence of basal-BR isolates in China. Here, we presented the first two complete genomic sequences of Chinese TuMV basal-BR isolates, WFLB06 and TANX2. The genomes of both isolates were 9833 nucleotides excluding the poly(A) tail, and had identical genomic structure. Most of their genes shared the highest identities with Japanese isolates. Recombination analysis showed that WFLB06 was an interlineage recombinant of basal-BR and Asian-BR parents, while TANX2 was an intralineage recombinant of basal-BR parents, and these two isolates represented two novel recombination patterns of TuMV. The ratio of nonsynonymous and synonymous substitution for the P1 gene of Chinese TuMV population was the highest and amounted to 12 times higher than that for the NIa-Pro gene, which implies that the selection pressure on the P1 gene was the highest among the genes present in the genome.

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The genetic structure of populations of Turnip mosaic virus in Kyushu and central Honshu, Japan

Cited by 18 publications

References 55 publications

Evolutionary trajectory of turnip mosaic virus populations adapting to a new host

Evolutionary trajectory of turnip mosaic virus populations adapting to a new host

Phylodynamic evidence of the migration of turnip mosaic potyvirus from Europe to Australia and New Zealand

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

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