Fig 1.
Symptoms associated with the shallot mild yellow stripe disease on shallot plant.
Table 1.
Number and percentages of high-throughput sequencing reads (73 nucleotides average length) of shallot virus X (variants 1 and 2), shallot latent virus, the novel carlavirus and the novel potyvirus in each sample analyzed by Illumina sequencing.
Fig 2.
Shematic representation of the genomic organization of the novel potyvirus (A) and the novel carlavirus (B). The open reading frames are depicted by large boxes, and the non coding regions (5’ and 3’ NCR) by horizontal lines. (A)n: PolyA tail. (A) The nine putative cleavage sites of the polyprotein are indicated, as well as the predicted amino acid position for each mature protein in the polyprotein. P1, helper component proteinase (HCPro), P3, 6K1, cylindrical inclusion (CI) protein, 6K2, viral genome-linked protein (VPg), nuclear inclusion a (NIa), nuclear inclusion b (NIb), and coat protein (CP). The position of PIPO (Pretty Interesting Potyviridae ORF) is also indicated. The black ellipse represents the VPg attached to the 5’ end of the genome. (B) Conserved motifs for viral methyltransferase (pfam 1660, Met), 2OG-Fe(II) oxygenase (pfam 03171, 2OG), peptidase C23 (pfam 05379, Pep), viral helicase 1 (pfam 01443, Hel), and RNA-dependent RNA polymerase 2 (pfam 00978, RdRp) domains are shown within replicase. TGB 1, 2, 3, Triple gene block proteins 1, 2, and 3. CP, coat protein. NABP, nucleic acid binding protein.
Fig 3.
Unrooted phylogenetic trees based on the codon-aligned nucleotide sequences of the 3’ part (from P3 to coat protein) of the polyproteins of representative Potyviridae family members (A) and on the coat protein sequences of representative members of the genus Potyvirus (B). The trees were constructed using the neighbor-joining method and statistical significance of branches was evaluated by bootstrap analysis (1,000 replicates). Only bootstrap values above 70% are shown. The scale bar represents 5% nucleotide divergence (A) or 5% amino acid divergence (B). The genus to which each virus belongs is indicated at the right of the panel A. The novel potyvirus shallot mild yellow stripe associated virus is indicated by a black star.
Fig 4.
Neighbor-joining phylogenetic tree reconstructed from the alignment of complete genome sequence of representative members of the families Alphaflexiviridae and Betaflexiviridae.
Statistical significance of branches was evaluated by bootstrap analysis (1,000 replicates) and only values above 70% are indicated. The scale represents 5% nucleotide divergence. The genus and the family to which each virus belongs are indicated at the right of the figure. The sequences of shallot virus X and shallot latent virus determined in this work are underlined, and the novel carlavirus shallot virus S is indicated by a black triangle.
Fig 5.
Comparison of the mean of symptom score (striping and loss of vigor) in two populations of shallot plants.
OYDV+/LYSV+/SMYSaV-: plants infected by onion yellow dwarf virus and/or leek yellow stripe virus and free of shallot mild yellow stripe associated virus. OYDV-/LYSV-/SMYSaV+: plants infected by shallot mild yellow stripe associated virus and free of onion dwarf virus and leek yellow stripe virus. Whiskers indicate the standard error of the mean. The significance (p) was tested by the Mann-Whitney-Wilcoxon non parametric test [20–21].