Fig 1.
Schematic representation of the putative genomic organization of fusariviruses.
The boxes and lines represent open reading frames (ORFs) and non-coding sequences, respectively. Positions of polymerase (Pol, red), helicase (Hel, green), and structural maintenance of chromosomes (SMC, blue) domains are indicated. Genomes are shown to scale. The A(n) represents poly (A) tail. Sodiomyces alkalinus fusarivirus 1 –SaFV1, Fusarium graminearum virus—FgV1, Sclerotinia sclerotiorum fusarivirus 1—SsFV1, Alternaria brassicicola fusarivirus 1- AbFV1,—Nigrospora oryzae fusarivirus 1—NoFV1. Fusarium poae fusarivirus 1 –FpFV1, Pleospora typhicola fusarivirus 1 –PtFV1, Rosellinia necatrix fusarivirus 1 –RnFV1, Penicillium roqueforti ssRNA mycovirus 1 –PrRV1, Macrophomina phaseolina ssRNA virus 1 –MpRV1, and Penicilium aurantiogriseum fusarivirus 1 –PaFV1, have similar genome organization as SaFV1.
Fig 2.
S. alkalinus isolates growing on alkaline agar plate.
Five days old isolates of S. alkalinus did not form inhibition zones or barrages between the strains although the mycelia did not fuse with each other.
Fig 3.
Phylogeny of the Sodiomyces sp. based on the ITS rDNA sequences (A), with the origin location of dsRNA-containing strains and phylogeny of the SaFV1 isolates based on the whole genome sequence (B).
Fig 4.
A) Double-stranded RNA profile of the virus-containing isolates F11, F12, F13, F18, and a virus-free isolate F7 of S. alkalinus. Viral dsRNAs are marked with arrows. M–DNA size standard. B) Detection of SaFV1 in isolates F13 and F7 by total RNA extraction and Northern blot analysis. Total RNA from virus-containing and virus-free isolates was extracted and resolved by electrophoresis in TAE gel, transferred to a nylon membrane, and probed with specific DIG-labelled probe corresponding nt positions 5026–5412 for SaFV1. The band of about 6.2 kb in size that match the SaFV1 genome size and faint band <4kb indicating the presence of subgenomic RNAs were detected (highlighted by arrows).
Fig 5.
Negative stained virus-like particles (highlighted by arrows) in the cellular extract of the S. alkalinus strain F13. Scale bar = 100 nm.
Fig 6.
The genomic organization of SaFV1 compared to other viruses that possess structural maintenance of chromosomes domain.
Boxes and lines represent open reading frames (ORFs) and non-coding sequences, respectively. Positions of polymerase (Pol, red), helicase (Hel, green), and structural maintenance of chromosomes (SMC, blue) domains are indicated. VP1-4 are structural proteins. Genomes are shown to scale.
Fig 7.
Phylogenetic tree of selected members of prokaryotic, eukaryotic, and viral SMC domains.
Phylogenetic ML-tree with Poisson correction with 1000 replications generated from SMC and SMC-like amino acid sequences. sequences (all used organisms and accession numbers of the sequences are shown in S3 Table). Bootstrap values are given at the nodes.
Fig 8.
Phylogenetic tree as inferred from the I-VII RdRp motifs of fusariviruses.
Maximum likelihood tree generated using RdRp segments of motifs I to VII with 1000 bootstrap replicates. Plum pox virus was used as an outgroup. Presence of the SMC domain in ORF2 protein of fusariviruses is indicated with an asterisk. Bootstrap values above 50% are given next to the branches. Section marks (§) indicate proposed taxa.
Table 1.
Presence of SMC domain in members of putative Fusariviridae family.
Position of the SMC domain on the ORF2 and E-value is presented.
Fig 9.
Potential secondary structures of 3´end, and ORF1-ORF2 intergenic region of Sodiomyces alkalinus fusarivirus 1 (SaFV1).
a) Potential secondary structures of 3´end (from 6183–6239 nucleotides) and b) ORF1-ORF2 intergenic region (from 4590 to 4659 nucleotides). The ΔG values (kcal/mol) were calculated using RNAfold program. UAA stop codons and AUG codon are marked.
Table 2.
Amino acid sequence identities (in %) of ORF1 (under the diagonal) and ORF2 (above the diagonal) between the SaFV1-containing isolates of S. alkalinus.
Fig 10.
Phylogeny of SaPV1 and CtParV1-SAL in relation to other partitiviruses.
ML phylogenetic tree generated from the RdRp amino acid sequence with 1000 bootstrap replicates.
Fig 11.
Phylogeny of SaPV1 and CtParV1-SAL in relation to other partitiviruses.
ML phylogenetic tree generated from the CP amino acid sequence with 1000 bootstrap replicates.
Table 3.
Comparative codon-usage analysis of viruses from S. alkalinus.
Frequency of [XYG + XYC] of S. alkalinus was computed from codon frequencies of RPB2 and TEF1-alpha protein coding genes sequenced previously [1], data for Colletotrichum sp. were from http://www.kazusa.or.jp.