Description of primers and probes used in real time PCR.

<p>Description of primers and probes used in real time PCR.</p

Origin of samples collected on tomato plants co-infected with TYX and TOX.

<p>Samples were collected from four independent experiments as indicated. Tomato plants were co-infected with <i>Tomato yellow leaf curl virus</i> (TYX) and <i>Tomato leaf curl Comoros viru</i>s;(TOX) either by agro-inoculation (blue lines) or by vector-inoculation (red lines). The vertical dotted red lines represent the vector transmission in which plant 1 and 4 were used as source plants. In Experiments 1–3, the percentage of recombinant genomes and the number of genomes analyzed (between brackets) were indicated at each sampling time. When the same recombinant genome was isolated from at least two distinct plants it is indicated by a symbol (▪, ▴, □) or by its name, (R10). (-) indicates no data obtained. In Experiment 4, the frequency of viral DNA of TYX and recombinant genomes (REC) in the viral population were estimated at 18 and 30 days post inoculation (dpi) by real time PCR. The frequency was estimated from the five plants which were detected positive for recombinants at 18 dpi and from the 22 plants detected positive at 30 dpi.</p

Frequency of TYX, TOX and recombinant (REC) genomes in co-infected tomato plants.

<p>Following co-infection of plants with <i>Tomato yellow leaf curl virus</i> (TYX) and <i>Tomato leaf curl Comoros virus</i> (TOX), the frequency of parental and recombinant genomes was monitored within plants at different days post-inoculation (dpi). <b>A</b>) Frequencies in four tomato plants co-infected by agro-inoculation and sampled at 30, 60 and 150 days post inoculation (dpi). The 330 dpi results were from four plants of a separate experiment as indicated in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058375#pone-0058375-g001" target="_blank">Figure 1</a>. <b>B</b>) Frequencies in five tomato plants co-infected by vector-inoculation and sampled at 60 and 150 days after the agro-inoculation of the source plants used for vector transmission as indicated in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058375#pone-0058375-g001" target="_blank">Figure 1</a>. The numbers at the top of the graphs indicate the total number of genomes analyzed by restriction analysis. The error bars are 95% confidence intervals of the mean frequency.</p

Relative infectivities of the recombinant R4 and the parental clones TYX and TOX in tomato.

<p>The infectivities were determined 30 days after co-inoculation of tomato plants with <i>Tomato yellow leaf curl virus</i> (TYX) and <i>Tomato leaf curl Comoros virus</i> (TOX) (A) or with TYX, TOX and recombinant R4 (B). Infectivity (number of infected plants/number of inoculated plants) was determined from four independent tests (1–4) comprising 30 to 45 plants each in (A) and 60 to 90 plants each in (B). In both graphs, the infectivity of TYX is arbitrarily set to 1 (blue line).</p

Effects of the co-inoculation method and the time after inoculation on the frequency of <i>Tomato yellow leaf curl virus</i> (TYX), <i>Tomato leaf curl Comoros vir</i>us (TOX) and recombinant genomes (REC) in co-infected tomato plants.

<p>Generalized linear mixed model, df = 1.</p>1<p>Significant effects (*) <i>P</i><0.05. (**) <i>P</i><0.001 and (***) <i>P</i><0.0001.</p

Percentage of recombinant genotypes sampled multiple times on tomato plants co-infected with <i>Tomato yellow leaf curl virus</i> (TYX) and <i>Tomato leaf curl Comoros virus</i> (TOX) at each of the sampling days post inoculation (dpi).

1<p>Within brackets: ratio of the total number of breakpoints in the distinct genotypes to the number of distinct genotypes.</p

Distribution of recombination breakpoints detected in viral genomes isolated from tomato plants co-infected with TYX and TOX.

<p>Recombinant genomes were isolated from tomato plant co-infected with <i>Tomato yellow leaf curl virus</i> (TYX) and <i>Tomato leaf curl Comoros virus</i> (TOX) and sampled at 60, 150 and 330 days post inoculation (dpi) as reported in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058375#pone-0058375-g001" target="_blank">Figure 1</a>. The distributions of recombination breakpoints are compared between genomes isolated at 60 dpi and 150 dpi from plants 4, 1V2 and 1V3 (<b>A, B, C</b>, respectively). Similarly, the distribution of breakpoints was compared between plants 5 and 6 at 330 dpi (<b>D)</b>. The breakpoints are presented on a genome linearized at the virion strand origin of replication and were located according to the nucleotide positions on the genome (x-axis). The positions of the six open reading frames (V1, V2, C1, C2, C3 and C4) are given at the top. The numbers in brackets indicate the numbers of genomes analyzed in each sample, followed by the number of distinct breakpoints among these genomes. The number of common breakpoints detected between recombinant genomes sampled from the same plant at two dates (<b>A-C</b>) or between two 330 dpi plants (<b>D</b>) is shown in black boxes. The y-axis indicates the number of genomes in which each breakpoint was detected.</p

Nucleotide positions in <i>Tomato yellow leaf curl virus</i> (TYX) and <i>Tomato leaf curl Comoros virus</i> genomes of restriction endonuclease restriction sites.

<p>The origin of virion strand replication is at position 1 for <i>Tomato yellow leaf curl vi</i>rus (TYX) and <i>Tomato leaf curl Comoros virus</i> (TOX).</p