The recombinogenic history of turnip mosaic potyvirus reveals its introduction to Japan in the 19th century

Abstract

Characterizing the detailed spatial and temporal dynamics of plant pathogens can provide valuable information for crop protection strategies. However, the epidemiological characteristics and evolutionary trajectories of pathogens can differ markedly from one country to another. The most widespread and important virus of brassica vegetables, turnip mosaic virus (TuMV), causes serious plant diseases in Japan. We collected 317 isolates of TuMV from Raphanus and Brassica plants throughout Japan over nearly five decades. Genomic sequences from these isolates were combined with published sequences. We identified a total of eighty-eight independent recombination events in Japanese TuMV genomes and found eighty-two recombination-type patterns in Japan. We assessed the evolution of TuMV through space and time using whole and partial genome sequences of both nonrecombinants and recombinants. Our results suggest that TuMV was introduced into Japan after the country emerged from its isolationist policy (1639-1854) in the Edo period and then dispersed to other parts of Japan in the 20th century. The results of our analyses reveal the complex structure of the TuMV population in Japan and emphasize the importance of identifying recombination events in the genome. Our study also provides an example of surveying the epidemiology of a virus that is highly recombinogenic.

Keywords: Japan; evolution; potyvirus; recombination; space and time; turnip mosaic virus.

Figure 1.

Sampling map of turnip mosaic virus (TuMV) Japanese isolates and maximum-likelihood tree inferred from polyprotein-coding sequences of 370 Japanese isolates. The aligned polyprotein-coding sequences are 9,486 nucleotides in length. Tree tips are connected to the sampling locations of the isolates. Outer lines show three major clades of Clade 1, 2, and 3. Colors of points on the map and connecting lines indicate recombination-type patterns, as shown in the key. Numbers at internal nodes indicate bootstrap percentages, based on 1,000 pseudoreplicates.

Figure 2.

A total of eighty-eight recombination events found in Japanese turnip mosaic virus (TuMV) genome with recombination frequency distribution across the genome. P value for recombination frequency was plotted against TuMV genome corresponding to the nucleotide position of UK1 isolate (Jenner et al., 2000). Dark and light grey shadow indicates the range of 95 per cent and 99 per cent confidence intervals, respectively.

Figure 3.

Phylogenetic tree of turnip mosaic virus (TuMV) inferred by maximum-likelihood from polyprotein-coding sequences of nonrecombinant isolates and sampling overview of Japanese isolates. (A) Tree of 184 nonrecombinant isolates including thirty-one Japanese nonrecombinant isolates newly found in this study. Of these, 153 isolates had been identified as nonrecombinant isolates in earlier studies (Yasaka, Ohba, and Schwinghamer et al. 2015; Yasaka, Fukagawa, and Ikematsu et al. 2017; Kawakubo, Gao, and Li et al. 2021). Numbers at internal nodes indicate bootstrap percentages, based on 1,000 pseudoreplicates. Triangles denote collapsed clades. Tip labels in red font indicate Japanese isolates, showing isolate name/prefecture of collection/district/year of collection. Tip labels in black font indicate isolates collected outside Japan, showing the country name of their collection. The polyprotein-coding sequences of the isolates of NLSYV (accession numbers JQ326210, JX156421, and NC_023628), NYSV (JQ395042, JQ911732, and NC_011541), JYMV (AB016500 and KJ701427), wild onion symptomless virus (NC_030391), and ScaMV (NC_003399) were used as outgroup taxa. The aligned polyprotein-coding sequences are 8,943 nucleotides in length. (B) Total numbers of TuMV nonrecombinant isolates and different recombination-type pattern (RTP) isolates in each sampling year. The classification of RTP is summarized in Supplementary Fig. S4. The Asian-BR × world-B3 interlineage recombinants are classified by the recombination type patterns as RTP1-3, RTP4-14, RTP15-26, and RTP27-33 based on the location of parental sequences of Asian-BR and world-B3.

Figure 4.

Dispersal history of nonrecombinants and recombinants of turnip mosaic virus. (A) Asian-BR × world-B3 interlineage recombinants; (B) basal-BR nonrecombinants and intralineage recombinants; and (C) world-B3 nonrecombinants and world-B2 × world-B3 interlineage recombinants. The polyprotein-coding sequences (aligned length 9,486 nucleotides) were used for this analysis. Upper panels show the year of the emergence and inferred dispersal routes. Inferred year of the emergence and 95 per cent credible intervals intervals are indicated above each recombination-type pattern (RTP). Large circles indicate the inferred root location for each recombination-type pattern, whereas small circles indicate the inferred locations of ancestral internal nodes and the sampling locations of the tips. Arrows indicate supported migration routes in discrete space. The 95 per cent credible interval areas of inferred internal nodes are projected based on 100 trees subsampled from the converged posterior samples and shown as different colored shadows by different recombination-type pattern. We only analyzed recombination-type patterns with more than six isolates, and the isolates of each recombination-type pattern are summarized in Supplementary Fig. S4. Lower panels show wavefront distance and mean dispersal speed averaged over their dispersal time. At each time point, the plot shows the spatial distance from the inferred root location of emergence. Dark lines and colored shadows indicate mean values and 95 per cent credible intervals, respectively. The dispersal speed of each recombination-type pattern in every ten years is summarized in Supplementary Table S7.