Laboratoire de Phytovirologie des Régions Chaudes, CIRAD/IRD, BP 5035, F-34032 Montpellier Cedex 1, France1
Laboratoire de Paléontologie, Paléobiologie et Phylogénie, Institut des Sciences de lEvolution (UMR 5554/CNRS), Université Montpellier II, Place E. Bataillon, F-34095 Montpellier Cedex 5, France2
Author for correspondence: Mustapha Bousalem. Fax +33 4 67 61 56 03. e-mail bousalem{at}mpl.ird.fr
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Abstract |
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Introduction |
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YMV is a highly destructive pathogen of yam (Dioscorea sp.) (Thouvenel & Fauquet, 1979 ; Thouvenel & Dumont, 1990
). YMV has been identified in all the areas of production (Africa, the Caribbean, Latin America and the South Pacific) and found in several species of Dioscorea. Yams are characterized by a very large diversity (603 species; Degras, 1993
), including a large number of wild taxa (Hamon et al., 1995
). Yam domestication started at least 5000 years ago (Dumont, 1982
) and the process is continuing, providing new sources of diversity. These characteristics, as well as its vegetative multiplication through tubers, its traditional cropping for centuries and the absence of sanitation, might favour virus evolution and diversification. Data on the evolution of YMV are scarce as variability analyses have been conducted on only a few samples collected from a restricted number of cultivars and species and as complete sequences of the coat protein (CP) and 3'-untranslated region (3'-UTR) are known for only one isolate (Duterme et al., 1996
; Aleman et al., 1996
; Aleman-Verdaguer et al., 1997
).
RNA virus diversity results from the accumulation of mutations due to frequent errors in RNA synthesis (Domingo & Holland, 1994 ; Drake, 1993
; Roossinck, 1997
). Recombination events are also a major evolutionary factor for RNA plant viruses (Simon & Burjarski, 1994
; Lai, 1995
; Aranda et al., 1997
). However, recombination has rarely been observed in natural populations and the frequency of recombinants has been reported for only a few viruses (Aranda et al., 1997
; Fraile et al., 1997
; Garcia-Arenal et al., 1997
). Recombination has previously been demonstrated for potyviruses by analysis of nucleotide sequences retrieved from the GenBank database (Revers et al., 1996
), and one recombinant has been found in a natural population of Plum pox virus (PPV) (Cervera et al., 1993
).
In this paper, we assessed the genetic diversity of YMV and evaluated the relative importance of the accumulation of mutations and RNA recombination in the evolution of this potyvirus in relation to its hosts. With this aim, (i) we sampled 27 YMV isolates on representative hosts including the most widespread species Dioscorea alata L., which is of Asian origin, the specific complex Dioscorea cayenensis Lam.Dioscorea rotundata Poir, which is of African origin and widely cultivated on this continent, and Dioscorea trifida L., which is restricted to its areas of origin, the Amazon and the Caribbean (Degras, 1993 ); (ii) we analysed the molecular variability of YMV isolates and compared it with that of other potyviruses, by sequencing the contiguous C-terminal part of NIb (C-Ter), the complete CP gene and the 3'-UTR; (iii) we assessed the molecular phylogeny of YMV, in relation to yam host species and cultivars and the geographical origin of the samples; and (iv) we developed the systematic detection of recombinant isolates.
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Methods |
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Phylogenetic analyses.
A region of 1184 nucleotides (nt) was sequenced for 27 isolates, including the contiguous 3'-terminal region of NIb (108 nt), the full CP (912 nt) and the 3'-UTR (164 nt). The complete NIbCP3'-UTR DNA and CP amino acid (aa) sequences were aligned and analysed by using the MUST package (Philippe, 1993 ). Within CP, we distinguished (i) the N-terminal region (N-Ter), encoding the hyper-variable N-terminal extension of the CP polypeptide (nt 1189, aa A1T63), (ii) the conserved core (nt 190879, aa H64E291) and the C-Ter region (nt 880912, aa R292M303).
Phylogenetic reconstructions were obtained by two complementary methods: (i) maximum parsimony (MP) (PAUP 3.1.1; Swofford, 1993 ), with all molecular characters assessed as independent, unordered and equally weighted (Fitch, 1971
); and (ii) maximum likelihood (ML) (Felsenstein, 1981
), using the quartet-puzzling method (PUZZLE 4.0; Strimmer & von Haeseler, 1996
), with the Tamura & Nei (1993)
model of sequence evolution and with a four-category gamma distribution of parameter
to describe substitution-rate heterogeneities (Yang, 1996
).
Robustness of the nodes of the phylogenetic trees was assessed by three different approaches: (i) the bootstrap (Felsenstein, 1985 ), yielding bootstrap percentages (BP) for each node, computed after 1000 resamplings followed by an MP reconstruction (bootstrap option in PAUP 3.1.1, with one random sequence addition per replicate and MAXTREES=100); (ii) the Bremer support index (BSI), the number of extra nucleotide or amino acid substitutions required to collapse the corresponding node (Bremer, 1988
), computed by the AUTODECAY 3.0 program (Eriksson, 1995
); and (iii) the reliability percentage (RP), the number of times the group appears after 10000 ML puzzling steps (PUZZLE 4.0; Strimmer & von Haeseler, 1996
).
To understand the pattern of nucleotide substitution in the CP gene better, the homoplasy and saturation of the two transitions and four transversions at each of the three codon positions were evaluated following the MP procedure of Hassanin et al. (1998) . Accordingly, we measured the consistency index (CI) and the slope (S) of the regression between the number of observed nucleotide differences and the number of inferred nucleotide changes for 18 substitution types. When the CI and S values are close to 1 (or close to 0), the corresponding substitution type is almost not (or strongly) homoplastic and saturated.
Recombination analyses.
Recombination events were suspected after performing comparisons of phylogenies reconstructed from the NIb, N-Ter CP, core CP and 3'-UTR regions. Three complementary statistical approaches were performed on the alignment of nucleotide sequences to maximize the probability of validation of the suspected recombination events. (i) The likelihood that genetic rearrangements had occurred was estimated by VTDIST (Sawyer 1989 ). This program omits conserved positions (condensation) and defines a set of fragments between successive informative sites for each sequence pair. Values of the sum of squares for the condensed fragments (SSCF) and the maximum length of the condensed fragments (MCF) were then compared after 10000 random permutations of sequences to provide an estimate of the likelihood of genetic rearrangements. (ii) The recombination break-points were tentatively localized by using the maximum
2 approach described by Maynard-Smith (1992)
, as implemented in RECSITE (Revers et al., 1996
). (iii) The recombinant sequences and the location of recombination junctions were detected by using PHYLPRO (version beta 0.8) developed by Weiller (1998)
. This program determines the pairwise distances of all aligned sequences at each position within a split window (optimal size for our data was 60 columns). To reduce the weight of rare point mutations, only phylogenetically informative sites were used to calculate the pairwise distances (parsimonious option). The correlation between these distances (phylogenetic correlation) ranged from +1 (perfectly correlated) to 0 (unrelated). They were plotted for all positions in a single graph to obtain the phylogenetic profiles, where recombination signals appeared as single, sharp downward peaks.
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Results and Discussion |
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This high level of variability of YMV CP was confirmed by a comparison between the intraspecies divergence of eight other potyviruses (177 CP sequences: Fig. 1). YMV was the potyvirus with the most variable CP, with an average divergence of 11·5% (aa).
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The high divergence values of the YMV CP placed some isolates between the strains of one potyvirus and closely related potyviruses in the tetramodal distribution of the family Potyviridae as described by Shukla et al. (1994) and Ward et al. (1995)
. Some PPV isolates also showed the same intermediate position, due to three individual isolates infecting particular host species, highlighting the role of the host in the selection of variants. In contrast to PPV, the high divergence of YMV is global and probably reflects a more complex evolutionary process, the major components of which are assessed below.
YMV variability is structured in distant phylogenetic relationships
To avoid any misleading conclusions due to the choice of phylogenetic reconstruction method, a 1184 nt region (NIb C-Ter, CP and 3'-UTR) of 27 YMV isolates was analysed by two complementary approaches, the equally weighted MP and the ML. A preliminary analysis was carried out with two distinct and closely related potyviruses as outgroups for YMV [PVY N strain, as used by Aleman-Verdaguer et al. (1997) , and Turnip mosaic virus QUE strain]. On the basis of 483 unambiguously alignable nucleotides of the CP core region, this analysis suggested that BFC56, BFC51, BFC54 and C1/C3 clustered together into group I and that they are the sister group of all isolates. On the basis of these results, subsequent reconstructions used group I as the outgroup.
Six additional major groups (groups IIVI and IX) were then indicated by high branch support (BP=100 and BSI ranging from +14 to +46) (Fig. 2a). The relative positions of isolates 608 and DIVIN were not well established and they were assigned to groups VII and VIII, respectively. The relationships between the major groups were not robustly resolved, except a basal position of CAM2 (group IX) and a sister-group position of group II relative to groups IIIVIII.
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Phylogenetic relationships of YMV isolates based on the CP gene showed the same groups as for the complete NIbCP3'-UTR sequences (Fig. 3). Analysis of CP amino acid sequences also yielded the same robust results (not shown). Pairwise sequence comparisons (Table 2
) confirmed the great divergence of groups I, II and IX, which showed the highest intragroup (up to 3·4% nt and 4·5% aa) and intergroup (17·922·0% nt and 14·818·3% aa) divergence. One should note that analysis of the C-Ter region of NIb detected these three groups with BP close to 100, although the region analysed was short (108 nt; data not shown).
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The lack of congruence between CP and 3'-UTR can be attributed not only to the restricted length of the 3'-UTR (low phylogenetic signal), but also to the difference in selection pressure between the coding and the non-coding regions and also to recombination events (see below). Within most virus genera, different genes usually have the same phylogenies, indicating that their evolution has been linked, that they have experienced the same speciation events and have co-diverged (Gibbs et al., 1997 ). In the case of the potyviruses, Aleman (1996)
showed that all phylogenetic trees based on every cistron of the potyvirus genome displayed a similar pattern. In the case of YMV, phylogenetic analysis carried out by Aleman-Verdaguer et al. (1997)
on six isolates showed the same topology whichever gene was studied, HC, NIb, P1, P3 or the partial CP region. These data consolidate our phylogenetic analysis based on the CP. Our results indicate that, in contrast, assessing phylogenetic relationships of potyviruses with the 3'-UTR is not recommended.
Low molecular evolutionary noise in the CP of YMV validates variability and phylogenetic analyses
Pairwise sequence comparisons to estimate genetic diversity as well as phylogenetic reconstruction may be highly sensitive to the evolutionary noise brought about by convergences and reversals (i.e. homoplasy). In protein-coding genes, such as the CP, multiple substitutions are known to occur in the third but also in the second codon positions (Naylor et al., 1995 ). To account for these homoplastic character-state changes and to evaluate their subsequent saturation through evolutionary time, weighting schemes have been proposed in order to reduce their effect in phylogenetic reconstruction (e.g. Hassanin et al., 1998
).
Because of the high rates of spontaneous mutation often reported for RNA genomes, it was especially important to measure the levels of homoplasy and saturation of each substitution type in our 27 YMV CP sequences (Table 3). The substitutions that were most subject to multiple changes were CT and AG transitions in the third codon position and, to a slightly lesser extent, in the first and second positions (range of CI and S values: 0·460·77). By contrast, all transversion types at all three codon positions were neither homoplastic nor saturated (range: 0·911·00). The overall pattern of substitution in the YMV CP showed that, according to the approach of Hassanin et al. (1998)
, there was no strong homoplasy or saturation in the data, thus validating the above-mentioned YMV variability (Table 2
) and phylogenetic (Figs 2
and 3
) analyses. Results of the MP analysis with character-state changes weighted by the product of CI and S values are not shown, but yielded similar branch support for the groups shown in Fig. 2(a)
, except for a more robust clustering of isolate 608 with group VI (BP=73).
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The most divergent groups (I, II and IX: Fig. 2) included isolates from Africa that infect D. cayenensisD. rotundata. However, as shown by the phylogenetic position of the POGNON isolate, members of the most diversified group, II (Table 2
), are now present in Guadeloupe and illustrate the spread of the virus by human activity. A robustly supported pole included the six other groups, with isolates infecting the three yam species coming from Africa, the Caribbean (Puerto Rico and Guadeloupe) and South America (French Guiana) (Fig. 2b
). In this clade, we observed a correlation between the clustering of the isolates and their geographical origin: groups III, IV and VII for Africa, groups VI and VIII for the Caribbean and group V for French Guiana.
A relationship between the phylogeny of the isolates and the yam species is not obvious, as members of the same phylogenetic groups (IV and VI) have been collected from two distinct hosts, D. cayenensisD. rotundata and D. alata (Fig. 2a). We should also note that the latter yam species may be infected by isolates affiliated to group II, as shown by the inclusion of the CP N-Ter region of isolate AIA from Guadeloupe (Aleman-Verdaguer et al., 1997
) in our phylogenetic analysis (not shown). In the case of D. trifida, however, a correlation was established with group V, as G5/C10, GY/INRA/C11 and G13/C1 have only been observed on this species (Table 1
and Fig. 2a
). Recent molecular and epidemiological data (not shown) obtained from the three yam species in the Caribbean and French Guiana confirmed this observation: isolates of group V collected in both these geographical areas were restricted to D. trifida. These results suggest the existence of a pathotype, which needs to be explored by biological assays. The case of isolate TRIFIDA/C5 will be discussed below.
To summarize, the phylogram of Fig. 2(a) suggests that the ancestral yam host for the 27 isolates studied is D. cayenensisD. rotundata and that independent transfers to D. alata and D. trifida have occurred during YMV evolution. Owing to the taxonomic controversy over the complex D. cayenensisD. rotundata, we distinguished between its two components: the perennial and semi-perennial yams of D. cayenensis and the annual yams of D. rotundata (Hamon & Touré, 1990
; Table 1
). The three divergent African groups were found on either D. cayenensis (groups I and II) or D. rotundata (group IX), whereas the other African groups (III and IV) included isolates from both D. cayenensis and D. rotundata.
Role of the host in selection of particular isolates: the Pilimpikou cultivar in Burkina Faso
A relationship between cultivar and molecular group was only established for group I members. BFC56, BFC51, BFC54 and C1/C3 infect a divergent cultivar (Pilimpikou) of the D. cayenensisD. rotundata complex, which may be related to the wild yam species Dioscorea abyssinica, Dioscorea lecardii and Dioscorea sagittifolia (R. Dumont & P. Hamon, unpublished data). In agreement with previous results (Duterme et al., 1996 ; Aleman-Verdaguer et al., 1997
), the CP N-Ter region of these isolates lacked 12 aa (CP positions 3748), but we could not conclude whether this was an ancestral or a derived deletion. Group I was also characterized by a mutation within the DAG block implicated in transmission by aphids. Three of the four isolates (BFC54, BFC51 and C1) showed a DTG motif instead of DAG. Analysis of other sequences of isolates from the same region (Duterme et al., 1996
; Aleman-Verdaguer et al., 1997
) confirmed the co-existence of populations with and without DAG. Different mutations in the DAG motif of potyviruses lead to the loss of transmissibility by aphids (Atreya et al., 1995
). Several transmission assays have shown the loss of this property from the Pilimpikou isolates (Urbino et al., 1998
). The region of Pilimpikou is isolated (200 km from other yam crops) and Pilimpikou is the sole yam cultivar cropped in this area. This situation reveals the adaptation of a natural virus population to a host and to particular ecological conditions.
Phylogenetic topological incongruence and statistical tests highlight recombination events
The comparison between phylogenies reconstructed from either CP and 3'-UTR or N-Ter and core plus C-Ter (Fig. 3) showed an incongruent position of three isolates, TRIFIDA/C5, CAM2 and 608, depending on the genomic area considered. This suggested the occurrence of recombination events during the evolution of YMV.
To evaluate the statistical significance of such events, to search for other recombinations not suggested by the topology of the trees and also to locate recombination break-points, complementary analyses were performed with VTDIST. The associated SSCF probabilities at the 5% level of significance are shown in Table 4. Several isolates showed significant associated SSCF probabilities in VTDIST analysis with the consensus sequence of group II (Table 4
). RECSITE and PHYLPRO analysis did not confirm these results and so it was difficult to consider them as putative recombinants. In particular, in agreement with Candresse et al. (1997)
, we found that the weight of particular point mutations in the subset of very close sequences could sometimes induce unreliable results. We will now discuss in more detail only the recombination events that were highlighted clearly by all the tests used.
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First evidence of multiple crossover recombination events in natural populations of a plant virus
In the case of the CAM2 isolate, the results are less straightforward. The CAM2 isolate displayed incongruent positions between the N-Ter and core region of the CP trees: it clustered with group II in the N-Ter tree (Fig. 3: RP=93, BP=76), but an affinity with groups IIVIII was rejected in the core plus C-Ter tree (RP=91, BP=100). Analysis of the C-Ter region of NIb confirmed the latter result, with BP close to 100 (data not shown).
VTDIST results suggested a potential recombination event with isolates of group I, but not with isolates of group II (Table 4). PHYLPRO results showed a more complex situation, with at least nine major peaks (Fig. 4
). One peak was located in NIb (nt 42), three peaks were located in the N-Ter region (nt 131, 191 and 279) and five in the core and C-Ter region (nt 309, 359, 405, 594 and 702). PHYLPRO analysis thus revealed a mosaic pattern of recombination. Two origins at least were clearly identified: group II in the N-Ter region of CP (upstream of nt 309) and group I in the core region of CP (upstream of nt 702).
The recombinant CAM2 represents the dominant population, as shown by direct sequencing. However, the sequences obtained after cloning revealed the co-existence of CAM2 in the same plant with the CAM2/C31 isolate, which is clustered in a different phylogenetic group (Figs 2 and 3
). This co-existence with other isolates is probably due to a secondary infection, which could be the source of multiple recombination events and could explain the difficulty in identifying the parents of the recombinant isolate.
To our knowledge, this is the first time that a mosaic pattern of recombination events has been observed in a natural population of a plant virus. This type of recombination has already been described in Murine hepatitis virus (MHV), a coronavirus, which contains a non-segmented RNA genome (Keck et al., 1987 ). In potyviruses, a single and a double recombinant have been detected recently when squash plants were co-bombarded with mixtures of engineered truncated constructs of Zucchini yellow mosaic virus (Gal-On et al., 1998
).
Both the 608 and DIVIN isolates, with ambiguous phylogenetic status, are recombinant isolates
Isolate 608 clustered with group VI in the CP region (Fig. 3: RP=83, BP=20), whereas it joined isolate B14 (group III) in the 3'-UTR region (RP=88, BP=54), with contrasting robustness values depending on the phylogenetic approach. However, the results of VTDIST analysis showed evidence of recombination events between 608 and isolates of groups II, IV and V and isolate DIVIN. Recombination involving isolates 174/C1 (group IV) and DIVIN was confirmed by both PHYLPRO (Fig. 4
) and RECSITE (P<0·001), but with different positions for the break-points.
The DIVIN isolate was linked to group V in the CP and N-Ter regions (Fig. 3: RP=87 and 91, respectively). However, phylogenetic conclusions about potential recombination could not be drawn, as the isolate was involved in a multifurcation in the trees derived from the 3'-UTR and core regions. The recombinant status of DIVIN was actually shown by pairwise analysis of VTDIST, with one parent belonging to group V (0·0003<P<0·008). The other parent could not be identified among our 27 sequences.
These results could explain the ambiguous phylogenetic status not only of isolate 608, but also of isolate DIVIN. An old recombination event followed by the accumulation of mutations on the recombinant sequence might have blurred the molecular signatures of both parents, leading to phylogenetic individualization of the recombinant itself during the evolution process. These two recombinants represent the dominant population, as shown by direct sequencing.
New perspectives on YMV origin and evolution
As demonstrated by our phylogenetic analyses, the African groups I, II and IX were the first to arise during the evolution of the 27 YMV isolates examined and might constitute the major YMV genetic pool. These three groups have a different origin, including an adaptation to a specific host and a multiple recombination event. Our results imply an African origin for YMV from numerous wild species at the origin of the D. cayenensisD. rotundata complex. We can attribute the large diversity observed to the differential accumulation of mutations and the significant contribution of recombination events.
Data on the evolution and history of the yam are essential for a better understanding of the diversification of YMV. In West Africa, man began to gather yams for domestic use as early as 50000 BC, but true yam-based agriculture started in approximately 3000 BC. The earliest movements of yam have been reported for Asiatic species (D. alata) in about 1500 BC from Malaysia to Africa, whereas the African species (D. cayenensisD. rotundata) moved westwards as far as America (Coursey, 1976 ). For this purpose, a study of YMV in relation to wild yam species in Africa and D. alata in its area of origin will be developed.
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Acknowledgments |
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This work was supported by the Institut de Recherche pour le Développement (IRD). The contribution of E.J.P.D. is no. 99-073 of the Institut des Sciences de lEvolution de Montpellier, UMR 5554 CNRS.
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Received 10 May 1999;
accepted 7 September 1999.