Figure 1 Electron micrograph of Potato spindle tuber viroid (PSTVd) and viral DNA (Coliphage T7 DNA) illustrating the comparative sizes and the rod-like structure of the viroid. The bar represents 0.5 µm (Reproduced from Diener, 1979).
Figure 2 Rod-like structure models for the different genera of the family Pospiviroidae. The type species of each genus is indicated on the right and the approximate location of the five domains C (central), P (pathogenic), V (variable) and TL and TR (terminal left and right), on top of the figure. The core nucleotides of the central conserved region (CCR), terminal conserved region (TCR) and terminal conserved hairpin (TCH), are shown. Arrows indicate flanking sequences which form, together with the core nucleotides of the CCR upper strand, imperfect inverted repeats. The core nucleotides of the Hop stunt viroid (HSVd) CCR have been defined by comparison with Columnea latent viroid (CLVd), which on the basis of other criteria (presence of the TCR, absence of the TCH, and overall sequence similarity) is included in the Pospiviroid genus. Substitutions found in the CCR and TCR of Iresine viroid 1 (IrVd-1), a new member of the genus Pospiviroid, are indicated in lowercase. In the genus Coleviroid the TCR only exists in the two largest members CbVd 2 and 3 (Adapted from Flores, Di Serio and Hernández, 1997).
Figure 3 Models for viroid replication. The plus polarity (solid lines) is assigned by convention to the most abundant infectious RNA and the minus polarity (open lines) to its complementary strand. The alternative asymmetric and symmetric pathways involve one and two rolling circles, respectively. In the symmetric variant, cleavage of plus and minus multimeric strands is mediated by hammerhead ribozymes (RZ), which lead to linear monomeric RNAs with 5-hydroxyl and 2-3-cyclic phosphate termini. Arrowheads denote the cleavage sites. The hammerhead structures that can be formed by Avocado sunblotch viroid (ASBVd), Peach latent mosaic viroid (PLMVd) and Chrysanthemum chlorotic mottle viroid (CChMVd) RNAs are shown on the right; conserved nucleotides are boxed. In the asymmetric variant, cleavage of plus multimeric strands may rely on a host factor (HF), which generates linear monomeric RNA containing probably 5-hydroxyl and 2-3-cyclic phosphate termini (Adapted with modifications from Flores, Di Serio and Hernández, 1997).
Figure 4 Consensus phylogenetic tree (based on 1000 replicates) obtained for viroids. ***, **, and *, group monophyletic in more than 95%, 85% and 75% of the replicates, respectively. Numbering of sequences was based on the similarities found between the upper strands of the central conserved regions of Pospiviroidae and the upper-left-hand portions of the hammerhead structures of Avsunviroidae (Diener, 1991). The alignment was performed with the Clustal X program, version 1.64 (gap opening and gap extension penalties 15 and 1, respectively) and minor manual adjustments between the conserved regions. Evolutionary distances were estimated according to the model of Jukes and Cantor and the phylogenetic tree was constructed by the neighbor-joining method using the MEGA program (version 1.01). Viroid genera are indicated on the right, and members belonging to families Pospiviroidae and Avsunviroidae are on white and dark backgrounds, respectively (De la Peña and Flores, unpublished data).
Figure 5 Primary and proposed rod-like secondary structure of lowest free energy for the reference sequence variant of Potato spindle tuber viroid (PSTVd) (Adapted with modifications from Gross, Domdey, Lossow, Jank, Raba, Alberty and Sänger, 1978).
Figure 6 Primary and proposed branched secondary structure of lowest free energy for the reference sequence variant of Peach latent mosaic viroid (PLMVd). Plus and minus self-cleavage domains are delimited by flags, the 13 conserved residues present in most of the hammerhead structures are indicated by bars, and the self-cleavage sites are shown by arrows. Solid and open symbols refer to plus and minus polarities respectively (Adapted from Hernández and Flores, 1992).
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