Schematic representation of the genome formula of <i>Faba bean necrotic stunt virus</i> (FBNSV) in two different host plant species.

<p>The genome formulae presented are in <i>Vicia faba</i> (A) and <i>Medicago truncatula</i> (B). The relative frequencies of the eight FBNSV segments have been calculated in within-host viral populations. The rounded median copy number of each segment is represented relative to the less abundant segment, here arbitrarily set to one. The core genome corresponds to the classical conception of a viral genome (rectangle). Adapted from reference [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005819#ppat.1005819.ref050" target="_blank">50</a>].</p

Summary of the families and genera of plant viruses with distinct virion structure, genome nature, and organization.

<p>Summary of the families and genera of plant viruses with distinct virion structure, genome nature, and organization.</p

Relationship between the phylogeny of movement proteins of the 30K superfamily and the genome organization of corresponding viruses.

<p>This tree was constructed from all movement protein sequences available at the time of reference [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005819#ppat.1005819.ref085" target="_blank">85</a>] using parsimony analysis. For more details on the construction of the tree, see reference [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005819#ppat.1005819.ref085" target="_blank">85</a>]. 0, RT, N, A, I, II, and III represent the type of polymerase encoded by the viruses: none, RNA-dependent DNA polymerase, negative-strand virus, ambisens-strand virus and positive-strand virus, and supergroups I, II, III RNA-dependent RNA polymerases, respectively. The thin-lined polygon encloses those movement proteins known to form virion-bearing tubules. Genera with a red asterisk are those whose member species are multipartite viruses (N.B.: The genus <i>Begomovirus</i> is composed of both monopartite and bipartite viruses). Reproduced and adapted from reference [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005819#ppat.1005819.ref085" target="_blank">85</a>].</p

Statistical analysis of the comparison of segment accumulation relative to R in leaves infiltrated with the eight FBNSV segments.

Comparisons of the accumulation of each segment relative to R to that of the others in leaves infiltrated with the eight segments were performed through Kruskal-Wallis tests using RStudio (package “agricolae”). The p-value indicating a statistically significant difference after Bonferroni correction (p≤0.05) is in red. (DOCX)</p

Comparison of DNA-R accumulation depending on the segment with which it was infiltrated.

The accumulation of DNA-R when infiltrated with each of the seven other segments (C+R, M+R, N+R, S+R, U1+R, U2+R or U4+R) or alone with the same (R) or doubled (R+R) OD of infiltrated bacteria was determined by qPCR. For each box, the horizontal central bar represents the median and the edges of the rectangle the first and third quartiles. The vertical outer bars delineate the minimum and maximum values of the distribution, excluding outliers. The dots represent outliers. Letters above the boxes indicate segments with which DNA-R accumulation is statistically significant (Kruskal-Wallis tests and Bonferroni correction for multiple tests; S8 Table). (TIF)</p

FBNSV segment accumulation in systemically infected or infiltrated leaves of <i>V</i>. <i>faba</i>.

V. faba young plants were stem-agro-inoculated with the eight segments of the FBNSV. DNA was extracted from systemically infected newly formed leaves four weeks later (grey). Alternatively, V. faba leaves were agro-infiltrated with DNA-R and one of the other seven segments (blue) or with the eight segments (orange). DNA was extracted from infiltrated areas six days later. Virus DNA accumulation in infiltrated and systemically infected leaves was estimated by qPCR. Leaf infiltration data were obtained from two different experiments. (A) The relative accumulation ratio of each segment with respect to DNA-R was calculated. For each box, the horizontal central bar represents the median and the edges of the rectangle the first and third quartiles. The vertical outer bars delineate the minimum and maximum values of the distribution, excluding outliers. The dots represent outliers. For a given condition (infiltration in pairs, infiltration of all segments or systemic infection) the statistically significant differences between segments were assessed with Kruskal-Wallis tests (p≤0.05; Bonferroni correction) and are indicated by different letters in grey (systemic infections), blue or yellow (infiltrations). (B) Relative frequencies of the segments in samples shown in (A): systemic infection (grey), infiltrated with R and another segment (blue) and infiltrated with the eight segments (orange). Relative frequencies in systemic infections match well with previous reports [1,10]. Standard deviations are represented by grey crosses (systemic infections), blue triangles (infiltration with R) or orange squares (infiltrations with the eight segments). Asterisks associated to segment names indicate when the differences in frequencies between systemic infections and infiltrations in pairs (blue) or infiltration of all segments (orange) are statistically significant. Differences were assessed with the Scheirer Ray Hare (p≤0.05) and post-hoc Dunn tests (Bonferroni correction).</p

Comparison of the FBNSV genome formula in complete and incomplete infections without C and/or U4.

FBNSV genome formula in incomplete infections FBNSVC-, U4- (blue) compared to FBNSVcomplete (A; grey) or FBNSVC- (B; red). Genome segments accumulation in symptomatic V. faba plants was estimated by qPCR and the relative frequency of the segments was determined. To allow meaningful comparisons, the relative frequency of each segment was calculated without considering the accumulation of segments C and U4 in FBNSVcomplete and without considering U4 in FBNSVC-. Standard deviations are represented by grey triangles (complete infections) or red crosses (incomplete infections). Asterisks associated to segment names indicate when the differences in frequencies between complete and incomplete infections are statistically significant (Scheirer Ray Hare (p≤0.05) and post-hoc Dunn tests, Bonferroni correction). (TIF)</p

Statistical analysis of the comparison of segment accumulation according to the condition.

For comparisons of the accumulation of each segment relative to R in each modality (systemic infections, leaf infiltration with pairs of segments or infiltrations with the eight segments), we first provide the output of a full model, ratio = modality * segment. This analysis was performed through Scheirer Ray Hare tests using RStudio (package “rcompanion”). After the full model tests we provide the output of per segment comparisons across pairs of modalities to identify segments whose relative frequency statistically significantly differed between modalities. The per segment differences were assessed through Dunn tests using RStudio (package “FSA”). The p-values indicating statistically significant differences after Bonferroni correction (p≤0.05) are in red. (DOCX)</p

S1 Fig -

Symptoms of V. faba infected with FBNSVcomplete (A and C) or FBNSVU2- (B and D) four weeks after agro-inoculation. (TIF)</p

Statistical analysis of the comparison of DNA-R accumulation depending on the segment with which it is infiltrated.

Statistical analyses were performed through Kruskal-Wallis tests using RStudio (package “agricolae”). The p-value indicating a statistically significant difference after Bonferroni correction (p≤0.05) is in red. (DOCX)</p