1 Laboratory of Plant Virology, Faculty of Agriculture, Saga University, Saga 840-8502, Japan
2 Laboratory of Animal Production and Management, Faculty of Agriculture, Saga University, Saga 840-8502, Japan
3 BioInfomatics Research Division, Japan Science and Technology Corporation, Tokyo 102-0081, Japan
4 Institute of Bioengineering, Zhejiang University of Science and Technology, Hangzhou Xiasha 310018, PR China
Correspondence
Kazusato Ohshima
ohshimak{at}cc.saga-u.ac.jp
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ABSTRACT |
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The GenBank/EMBL/DDBJ accession numbers of the nucleotide sequence data obtained in this study are AB179888AB180040.
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INTRODUCTION |
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Turnip mosaic virus (TuMV) infects a wide range of plant species, mostly from the family Brassicaceae. It is probably the most widespread and important virus infecting both crop and ornamental species of this family and occurs throughout the world, including the temperate and tropical regions of Africa, Asia, Europe, Oceania and North and South America (Provvidenti, 1996; Ohshima et al., 2002
). TuMV was ranked second only to Cucumber mosaic virus (CMV) as the most important virus infecting field-grown vegetables in a survey of virus disease in 28 countries and regions (Tomlinson, 1987
; Walsh & Jenner, 2002
). TuMV belongs to the genus Potyvirus. This is the largest genus of the largest family of plant viruses, the Potyviridae (Riechmann et al., 1992
; Shukla et al., 1994
; Berger et al., 2000
), which itself belongs to the picorna-like supergroup of viruses of animals and plants. TuMV, like other potyviruses, is transmitted by aphids in a non-persistent manner (Hamlyn, 1953
). Potyviruses have flexuous filamentous particles, 700750 nm long, each of which contains a single copy of the genome, which is a single-stranded positive-sense RNA molecule about 10 000 nt long. The genomes of potyviruses have terminal untranslated regions between which is a single open reading frame that is translated into a single large polyprotein. This is hydrolysed into several proteins by proteases that are part of the same polyprotein (Riechmann et al., 1992
). Potyvirus P1 genes, the most variable in the potyvirus genome, encode a serine proteinase (Verchot et al., 1992
; Choi et al., 2002
), which is also the most variable potyvirus protein (Tomimura et al., 2003
), but the precise function of P1 in viral infections has not yet been established. Neither has the function of the P3 gene (Urcuqui-Inchima et al., 2001
; Jenner et al., 2002
, 2003
). The other proteins encoded by potyvirus genomes are relatively conserved, although the N termini of the CP genes are also variable.
There have been two reports of studies of the phylodemography of TuMV (Ohshima et al., 2002; Tomimura et al., 2003
). Comparisons of genomic sequences showed that TuMV isolates fell into four well-defined close-knit groups: basal-B, basal-BR, Asian-BR and world-B. Parts of around one-fifth of the sequences were phylogenetically anomalous, and this was shown to have resulted from recombination, which seemed therefore to be a significant generator of genetic diversity in populations of this virus. Interestingly, the clear recombinants were found only in isolates from east Asia, and uncertain recombinants, perhaps more ancient, were found only in lineages from other parts of the world.
In the study reported here, we analysed a total of 89 representative TuMV genomic sequences (on average about one-third of each) using methods based on different evolutionary assumptions, and we discuss the results in terms of the information they provide on the extent to which recombination drives the evolution of TuMV populations.
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METHODS |
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Sequencing.
Nucleotide sequences of the genes encoding P1, the C terminus of cylindrical inclusion (Ct-CI) (from nt 5680 to the 3' end of this gene as described for the 1J nucleotide sequence; Ohshima et al., 1996), 6K2, NIa-VPg and NIa-Pro and the coat protein (CP) of each isolate were determined from two independent RT-PCR products and cloned plasmids. Each cloned plasmid and RT-PCR product was sequenced by primer walking in both directions using the BigDye Terminator v3.0 Cycle Sequencing Ready Reaction kit (Applied Biosystems) and an Applied Biosystems Genetic Analyzer DNA model 310; ambiguous nucleotides in any sequence were checked in sequences obtained from at least four other independent plasmids. Sequence data were assembled using BioEdit version 5.0.9 (Hall, 1999
).
Recombinant analyses.
The sequences of 70 Asian and 19 non-Asian TuMV isolates (Tomimura et al., 2003), a total of 89, were used for evolutionary analyses. First, we joined the nucleotide sequences of the P1, Ct-CI, 6K2, NIa-VPg, NIa-Pro and CP genes, and termed this the P1+R12+Pro+CP region. Among the 29 phylogenies obtained from the aligned gene sequences or genomic slices, only those from the region around nt 55016500 in degapped sequences, which we call region 12 (R12; see Tomimura et al., 2003
), and which extends from Ct-CI to the middle of the NIa-Pro sequences, were almost identical to those constructed from entire genomic sequences in all three maximum-likelihood (ML), maximum-parsimony (MP) and neighbour-joining (NJ) trees. Therefore, we joined the R12 sequences between P1 and the remainder of NIa-Pro+CP sequences to produce P1+R12+Pro+CP sequences of each isolate for further evolutionary analyses. The homologous regions of two sequences of Japanese yam mosaic virus (JYMV) (Fuji & Nakamae, 1999
, 2000
), one of Scallion mosaic virus (ScaMV) (Chen et al., 2002b
) and one of Narcissus yellow stripe virus (NYSV) (Chen et al., 2003
) were used to align the TuMV P1+R12+Pro+CP sequences, as BLAST searches had shown them to be the sequences in the international sequence databases most closely and consistently related to those of TuMV; TuMV P1 genes were more closely related to those of JYMV than ScaMV, whereas for many other TuMV regions/genes such as R12+Pro the converse was true, except that the TuMV CP gene is most closely related to that of NYSV. We thus aligned all 89 P1 sequences with those of two JYMV isolates as the outgroup, the R12+Pro sequences with those of JYMV and ScaMV and the CP sequences with that of NYSV, using CLUSTAL X (Jeanmougin et al., 1998
). However, this procedure resulted in some gaps that were not in multiples of 3 nt. Therefore, the amino acid sequences corresponding to individual regions with the appropriate outgroups indicated above were aligned using CLUSTAL X with TRANSALIGN (kindly supplied by Georg Weiller) to maintain the degapped alignment of the encoded amino acids and then reassembled to form sequences 3324 nt long. The aligned sequences were checked using SISCAN version 2 (Gibbs et al., 2000
) and PHYLPRO (Weiller, 1998
) for incongruent relationships that might have resulted from recombination. These analyses also assessed which non-recombinant sequences have regions that are closest to regions of the recombinant sequences and hence indicate the likely lineages that provided those regions in the recombinants. For simplicity in this paper, we call these the parental isolates of recombinants, although they are merely those that include the most closely related regions. The transversion and transition rates of all pairs of sequences were calculated using DAMBE (Xia & Xie, 2001
).
Phylogenetic analyses.
Two JYMV sequences and one from ScaMV were used as an outgroup to construct a P1+R12+Pro+CP phylogenetic tree, because the CP sequence of only one NYSV isolate has been published (Chen et al., 2003). The phylogenetic relationships of the sequences were determined by three methods: the ML algorithm of TREEPUZZLE version 5.0 (Strimmer & von Haeseler, 1996
; Strimmer et al., 1997
), the MP algorithm of PAUP 4.0 beta version 10 (Swofford, 1998
) and the NJ algorithm of PHYLIP version 3.5 (Felsenstein, 1993
). For ML analyses, 1000 puzzling steps were calculated using the HasegawaKishinoYano (HKY) model of substitution (Hasegawa et al., 1985
). For MP analyses, the heuristic search option and 1000 bootstrap resamplings were used. For NJ analyses, distance matrices were calculated by DNADIST with the Kimura two-parameter option (Kimura, 1980
), and trees were constructed from these matrices by the NJ method (Saitou & Nei, 1987
). A bootstrap value for each internal node of the NJ trees was calculated using 1000 random resamplings with SEQBOOT (Felsenstein, 1985
). The calculated trees were displayed by TREEVIEW (Page, 1996
). Nucleotide and amino acid similarities were estimated using the Kimura two-parameter method (Kimura, 1980
) and Dayhoff PAM matrix (Dayhoff et al., 1983
), respectively.
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RESULTS |
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Recombination sites
In a previous study we showed that at least 10 % of 76 TuMV isolates had recombinant P1 and CP genes (Ohshima et al., 2002) and that these caused inconsistencies in phylogenetic analyses and poor bootstrap support for some lineages in the resulting trees. Therefore, we first checked the P1+R12+Pro+CP sequences for evidence of recombination. After gaps had been removed, the phylogenetic profiles' of the sequences were examined using PHYLPRO (Weiller, 1998
). This clearly showed that parts of some sequences were phylogenetically anomalous, in that different parts of them had different phylogenetic affinities (data not shown). Proof that these anomalies resulted from recombination rather than convergent selection was obtained by the sister scanning method (Gibbs et al., 2000
). All the isolates that had been identified as recombinants in the P1+R12+Pro+CP region by Tomimura et al. (2003)
had statistically significant conflicting related signals' (CRSs) in sites that differed synonymously from those in other sequences. Many isolates seemed to have significant CRSs that differed synonymously in the middle of the P1 gene. It was found, for example, that isolate HOD517J was most closely related (Z-values>3·0) to sequence CHN5 in the N-terminal half of the P1 gene (nt 250520), but that the C-terminal half (nt 520850) was closer to CHBJ1 in total nucleotide and synonymous and non-synonymous site analyses (for synonymous site analysis, see Fig. 1
a).
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Phylogenetic relationships
We calculated trees from the concatenated P1+R12+Pro+CP sequences of the 89 isolates, including all clear recombinants identified previously (Ohshima et al., 2002; Tomimura et al., 2003
) and in this study. We investigated the relationships of the isolates by three methods (ML, MP and NJ) but only the ML tree is shown (Fig. 2
). All the trees partitioned most of the sequences into the same four consistent groups: basal-B, basal-BR, Asian-BR and world-B.
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Table 2 lists the probable recombination sites in the P1+R12+Pro+CP region as indicated by SISCAN, together with the parental (the closest isolate) sequences. The many isolates that had significant CRSs in sites that differed synonymously from those in other sequences in the middle of the P1 gene were mostly Asian. One cross-over site, nt 350400, was found only in two Nepalese isolates, whereas the two other sites, nt 450500 and nt 500550, were found in Chinese/Japanese/Korean isolates or Chinese/Japanese isolates, respectively. All these isolates were strain BR and were recombinants of world-B and Asian-BR parents; furthermore, the closest parental isolates of the recombinants had all been collected in China. We looked in more detail at the sequences around the recombination sites in the P1 gene and some, including two that were found Asia-wide. Nt 478493 and nt 503517, corresponding to aa 159164 and aa 168173 in the encoded amino acid sequences, were likely to be recombination sites (data not shown). On the other hand, many isolates analysed in this study by SISCAN had CRSs at the junction between the P1 and Ct-CI genes and/or in the NIa-VPg gene. For instance, the CHL13, CHL14 and RHS1 isolates seemed to have recombination sites within the P1 gene and between the P1 and Ct-CI genes, and were recombinants of world-B, Asian-BR and basal-BR parents. Many of the other sequences, notably A102/11, ITA7, St48 and IS1 from the basal groups and CHN12, CHYK56, CHK55, CHZJ27, Ka1J, DMJ and RAD1 from the world-B group, had recombination sites in their P1 and NIa-VPg genes when examined by SISCAN using synonymous differences, but these were not clear recombinants. Table 3
summarizes the numbers of isolates which have recombination sites within different subpopulations and in different genes/regions. In particular, many Asian isolates were recombinants whether they were strain BR or B. The recombination sites in the BR isolates were found mainly in the P1 and NIa-VPg genes, and also between the P1 and Ct-CI gene/region, whereas B strain recombination sites were found mostly at the junction of the P1 and Ct-CI gene/region. However, careful analyses using representative entire sequences are necessary to identify recombination sites between the junction of P1 and the Ct-CI gene/region.
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DISCUSSION |
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An earlier study of the entire sequences of 38 isolates had shown that eight were recombinants and five multiple recombinants, namely three double, one triple and one quadruple (Tomimura et al., 2003). All these isolates had been collected in Asia and this led us to collect more samples from Asian populations to determine more accurately how common recombinants were in those TuMV populations. An earlier study of the P1/CP genes (Ohshima et al., 2002
) showed that only two isolates, 1J and FD27J, from the Asian population (5 %) had clear recombination sites in their P1 genes, whereas in this study we found that 21 of 70 Asian isolates (30 %) had recombinant P1 genes, as did 21 of 45 Asian strain BR isolates (47 %) (Table 3
). This study also showed that 57 of 89 isolates (64 %) were recombinants of the P1+R12+Pro+CP region (Fig. 2
), although it will be necessary to analyse this region for more isolates, including non-Asian regions and especially Europe, to assess accurately the number of recombinants in all TuMV populations. So why did we find a larger proportion of recombinants in the work reported here? One possible cause is sampling bias, as more Asia-wide isolates were analysed in this study than in previous studies and the new samples came from more widely distributed sites, so more between-population recombinants were detected. Our results indicate that it is important to analyse representative numbers of isolates collected in at least two neighbouring parts of the same biogeographical region. Bateson et al. (2002)
found a similar population structure in studies of populations of Papaya ringspot virus, another potyvirus; major lineages revealed the pattern of worldwide migration, whereas in south-east Asia and the western Pacific there was a single mixed population with some well-defined subpopulations.
We analysed recombinants in the P1 genes not only of the 89 sequences listed in Table 1 but also of the sequences available in the international sequence databases, 124 isolates in all (data not shown). Six Japanese isolates showed anomalies in SISCAN synonymous site analyses and had clear recombination sites within their P1 genes, indicating that all Japanese Asian-BR group isolates examined so far are recombinants. In addition, because PHYLPRO and SISCAN are sliding window methods, it is not possible to analyse fully the N termini of P1 sequences using only P1 sequences; we therefore joined the 5'NCRs and P1 sequences of each isolate and then analysed them by SISCAN. In BLAST searches, the TuMV 5'NCR was most closely related to the homologous region of the genome of Plum pox virus (PPV); we thus aligned them by CLUSTAL X using not only JYMV or ScaMV but also PPV as members of an outgroup and joined the degapped aligned 5'NCR sequences to the TuMV P1 sequences that had been aligned using only the two JYMV sequences as an outgroup. When we analysed these sequences for phylogenetic anomalies using all the nucleotide sites, most but not all of the Asian isolates had recombination sites almost at the N terminus of the P1 gene (nt 112; from the beginning of degapped P1 sequences) and with the most closely related parental sequences from the Asian BR and world-B groups (data not shown). Unfortunately, the recombination sites were located near the junction of the 5'NCR and P1 sequences, so we could not analyse them using synonymous or non-synonymous sites separately, and could not assess whether or not these are clear recombination sites at the 5' end of the P1 gene. Phylogenetic analyses of the aligned P1 sequences showed that many strain BR recombinants had world-B group sequences between nt 141 and 605 and Asian-BR group sequences between nt 752 and 1086 (Fig. 3
). In all, 47 % of BR strains had mosaic P1 genes (Table 3
). Our sequence comparisons provided no clear functional explanation for the large proportion of P1 mosaic structures. It is possible that recombinants may adapt more quickly to new hosts or have enhanced pathogenicity or P1/HC-Pro fusion (Kasschau & Carrington, 1998
; Urcuqui-Inchima et al., 2001
). The newly identified recombination sites in the P1 and NIa-VPg genes were most common in the emerging Asian subpopulation and in BR strains, and our comparisons also show that most recombination sites in TuMV genomes are found in the P1 and NIa-VPg genes, which are, respectively, the most variable and relatively well-conserved genes of potyvirus genomes. The P1 protein is also the most variable of potyvirus proteins but the reason for this is at present unknown (Shukla et al., 1994
; Urcuqui-Inchima et al., 2001
), although it may result from recombination, as the recombinants we found in the P1 gene all had parents from different lineages (world-B and Asian-BR), whereas recombinants in the NIa-VPg gene mostly had parents from the same lineage (Asian-BR and Asian-BR).
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Among 57 Asian recombinants, 60 % were intralineage recombinants and 40 % were both interlineage and intralineage recombinants, and most of the latter were at least triple recombinants (Fig. 3). For instance, the isolates in recombinant types K and M were likely to be parents of the isolates in recombination type J, and seemed to be at least double recombinants. Thus, some of the intralineage recombinants seemed to be both parent and progeny, and detailed comparisons of these recombination sites may be required in order to reveal the order of events. One of two recombination sites within the P1 gene found in this study was around nt 727 and was found in two Chinese isolates (collected in Beijing), a Korean isolate and six Japanese isolates (all from Kyushu in south-west Japan), locations that are close to one another. The other recombination site around nt 752 was found in Chinese and Japanese isolates, and collected in Guilin (mid-south of China) and all parts of Japan (Fig. 3
, Table 2
). Therefore, this latter group of Asian TuMV isolates, all BR strains and collected in different countries, share recombination sites in their P1 genes that probably came from a single recombination event. Studies of Puumala virus (Sironen et al., 2001
) and HIV-1 (Cornelissen et al., 2000
) have also shown how recombinants provide information from which the migratory spread of hosts and viruses may be deduced. Therefore, although it is not possible to exclude the possibility that some of the recombination sites found in Asia-wide isolates are in recombinational hotspots, we believe that it is more likely that they come from a limited number of recombinational events and, together with sequence similarities, usefully trace the migration and evolution of this virus.
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ACKNOWLEDGEMENTS |
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Received 22 March 2004;
accepted 25 May 2004.