Figure 1.
Simplified schematic of the genomic organization of the Secoviridae.
The names of eight taxa are indicated on the right of the depicted genomes. The monopartite genomes of the waikaviruses and sequivirus are diagrammed at the top from left to right in a 5’ to 3’ direction. Only the protein-encoding regions are shown, delineated as shaded rectangles. The remaining taxa/genera have bipartite genomes. The functional domain order in the two RNAs is conserved and they are displayed with the RNA2 on the left, separated from the RNA1 by a solid vertical line. This arrangement allows the coding regions of the bipartite viruses to be aligned with the monopartite genomes. The functional regions from left to right are: the putative movement protein or 2N terminal protein 2N(MP), the coat protein (CP), the putative protease cofactor or 1N terminal protein 1N(ProCo), the helicase (HEL), the protease (Pro) and the RNA-dependent RNA polymerase (RdRp). Putative additional N-terminal genes are shown with dotted borders for the genera Nepovirus (of various sizes depending on subgroup), Sadwavirus and Torradovirus. The existence of a translation product or function for the latter virus has still not been demonstrated and was thus excluded from the analyses. * indicates the putative 5'-genome-linked protein (VPg). Black raspberry necrosis virus (BRNV), Strawberry latent spherical virus (SLRSV), Strawberry mottle virus (SMoV).
Table 1.
List of Secoviridae isolates and related sequences used in the analyses, including their acronyms and Genbank accession numbers.
Table 2.
Selection and diversity for coat protein (CP) of secovirid species.
Figure 2.
Estimates of the nucleotide substitution rates per site for the coat proteins of nine secovirids.
Arabis mosaic virus (ArMV), Bean pod mottle virus (BPMV), Broad bean wilt virus-2 (BBWV-2), Blackcurrant reversion virus (BRV), Grapevine fanleaf virus (GFLV), Rice tungro spherical virus (RTSV), Strawberry mottle virus (SMoV), Tomato ringspot virus (ToRSV) and Tobacco ringspot virus (TRSV). Real (time-tipped) mean values (black horizontal bars) are aligned with randomized (gray horizontal line) with the 95% highest posterior density (HPD) ranges for each depicted by the vertical bars. * - estimates considered statistically solid based on mean values being outside the range of the randomized HPD. Substitution rates for data spreading less than 10 years (BRV and SMoV) or where the HPD ranges was larger in the randomized than in the time-tipped calculations (TRSV) (See Table 3) are not depicted. On the right are depicted the mean substitution rate distributions for coat proteins of the Luteoviridae (green bar) (Pagan and Holmes 2011), and the VP1 of Picornaviridae (Hicks and Duffy, 2011).
Table 3.
Calculated Nucleotide substitution rates and Time from Most Recent Common Ancestor (TMRCA) for members of the Secoviridae.
Figure 3.
Coalescent tree for the subfamily Comovirinae using coat protein sequences.
Bayesian priors were set for a lognormal relaxed molecular clock at the most conservative mean species nucleotide substitution estimate of 2.74×10-3 (for ToRSV) using a constant tree prior with all species’ sequences ‘time-stamped’. Horizontal blue bars show the 95% highest posterior density (HPD) ranges for each node. The presence of the HPD bar denotes a node posterior probability greater than 0.9. Arabis mosaic virus (ArMV), Bean pod mottle virus (BPMV), Broad bean wilt virus-2 (BBWV-2), Blackcurrant reversion virus (BRV), Grapevine fanleaf virus (GFLV), Tomato ringspot virus (ToRSV) and Tobacco ringspot virus (TRSV). The equivalent tree generated using a strict clock is shown in the supplemental data.
Figure 4.
Maximum likelihood inferred phylogenetic trees for the six main functional domains of the Secoviridae.
The putative movement protein or 2N terminal protein, 2N(MP); the coat protein (CP); the putative protease cofactor or 1N terminal protein, 1N(ProCo); the helicase (HEL), the protease (Pro), and the RNA-dependent RNA polymerase (RdRp). Designated viral lineages are contained within the polygons, in descending order: green, Comovirinae; blue, Nepovirus; yellow, Fabavirus; yellow/green, Comovirus; orange, Sadwavirus; red/green, Cheravirus; grey, Sequivirus, Waikavirus; red, Torradovirus. Numbers at nodes refer to bootstrap values, with any branch below 70% being collapsed. The outgroup (black oval) for all trees is the corresponding functional gene of the Potato virus Y (PVY). PVY is type member of the potyvirus genus in the Potyviridae family – a group of plant infecting picorna-like viruses that lies outside the Picornavirales order [74]. Apple latent spherical virus (ALSV), Arabis mosaic virus (ArMV), Bean pod mottle virus (BPMV), Beet ringspot virus (BRSV), Black raspberry necrosis virus (BRNV), Blackcurrant reversion virus (BRV), Broad bean wilt virus-1 (BBWV1), Broad bean wilt virus-2 (BBWV2), Cherry rasp leaf virus (CRLV), Cowpea mosaic virus (CPMV), Cowpea severe mosaic virus (CPSMV), Cycas necrotic stunt virus (CNSV), Grapevine chrome mosaic (GCMV), Grapevine fanleaf virus (GFLV), Maize chlorotic dwarf virus (MCDV), Parsnip yellow fleck virus (PYFV), Radish mosaic virus (RaMV), Red clover mottle virus (RCMV), Rice tungro spherical virus (RTSV), Satsuma dwarf virus (SDV), Squash mosaic virus (SqMV), Strawberry mottle virus (SMoV), Strawberry latent ringspot virus (SLRSV), Tobacco ringspot virus (TRSV), Tomato marchitez virus (ToMarV) and Tomato ringspot virus (ToRSV), Tomato torrado virus (ToTV).
Figure 5.
Schematics of the amino acid similarities four functional domains of members of the Secoviridae.
These proteins are: on RNA1 (a), the putative protease cofactor or 1N terminal protein 1N(ProCo), the protease (Pro), and on RNA2 (b) the putative movement protein or 2N terminal protein 2N(MP), and the coat protein (CP). The analyzed proteins are those from five lineages of secovirids, the species Apple latent spherical virus (ALSV), Arabis mosaic virus (ArMV), Bean pod mottle virus (BPMV), Beet ringspot virus (BRSV), Black raspberry necrosis virus (BRNV), Blackcurrant reversion virus (BRV), Broad bean wilt virus-1 (BBWV1), Broad bean wilt virus-2 (BBWV2), Cherry rasp leaf virus (CRLV), Cowpea mosaic virus (CPMV), Cowpea severe mosaic virus (CPSMV), Cycas necrotic stunt virus (CNSV), Grapevine chrome mosaic (GCMV), Grapevine fanleaf virus (GFLV), Maize chlorotic dwarf virus (MCDV), Parsnip yellow fleck virus (PYFV), Radish mosaic virus (RaMV), Red clover mottle virus (RCMV), Rice tungro spherical virus (RTSV), Satsuma dwarf virus (SDV), Squash mosaic virus (SqMV), Strawberry mottle virus (SMoV), Strawberry latent ringspot virus (SLRSV), Tobacco ringspot virus (TRSV), Tomato marchitez virus (ToMarV) and Tomato ringspot virus (ToRSV), Tomato torrado virus (ToTV). In the lower light gray shaded hemisphere are the animal infecting families of the order Picornavirales, which excludes the picorna-like virus families Caliciviridae and Potyviridae. The outer broken black circle shows the clustering of related viruses in different secovirus lineages. Similarities were determined using the BLAST and PSI-BLAST algorithms; details of the PSI-BLAST are listed in table 4. Viruses depicted were selected based on the highest scoring sequence for each species (within the Secoviridae) or family (among the picorna-like viruses) with only one sequence hit being shown irrespective of the number identified by the program. Secovirids not included in primary analysis were only marked on the figure when they were the only representative that was a hit. For each taxon shown, Blast hits are depicted in favor of PSI-BLAST hits, PSI-BLAST hits only being shown in the absence of a Blast hit.
Figure 6.
Host distribution of known related virus sequences.
a) three putative models for assigning directionality of colonization based on diversity (proportional to the diameter of circle); the greater the diversity the older the population. In model three the distributions have reached an ‘equilibrium’ due to the limits of detection (ie the most divergent viruses cannot be identified), b) the distribution of the total number (in parentheses) of recognized ICTV classified viruses according to eukaryotic host. c) distribution, within the framework of the models proposed in a), of related ICTV-recognized virus species (black numbers) for the coat protein (CP, left) and the protease (Pro, right). Circles are proportional to number of species (orange – vertebrate host, blue – insect host). Arrow sizes are proportional to the ratio of the number of species in each host type (e.g. animal species:plant species or plant species:animal species). Absence of the thin black vertical line means that no significant animal homolog was identified. The rounded blue boxes contain members of the subfamily Comovirinae. Broad bean wilt virus-1 (BBWV1), Cherry rasp leaf virus (CRLV), Grapevine fanleaf virus (GFLV), Rice tungro spherical virus (RTSV), Strawberry mottle virus (SMoV), Strawberry latent ringspot virus (SLRSV), Tobacco ringspot virus (TRSV), and Tomato torrado virus (ToTV).
Figure 7.
Putative model of colonization of plants by the Secoviridae.
Cherry rasp leaf virus (CRLV), Rice tungro spherical virus (RTSV), Strawberry mottle virus (SMoV), Strawberry latent ringspot virus (SLRSV), Tomato torrado virus (ToTV). Time scale of years increasing from right to left. Upon first introduction from vectors into plants, the viruses can replicate, but are not able to move from cell-to-cell (schematically shown as polygons with dashed lines). Upon acquisition of a movement protein (MP, shown as red square), viruses (schematically shown as polygons with solid lines) are then more effectively able to move cell-to-cell and systemically infect the plant host.