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Fig. S1 Predicted secondary structures of the three Citrus exocortis viroid (CEVd) variants used in this study. The most stable structures of CEVd.188, as predicted by Mfold (A) and RNAstructure 5.1 (B), of CEVd.189, as predicted by Mfold (C) and RNAstructure 5.1 (D), and of CEVd.190, as predicted by Mfold (E) and RNAstructure 5.1 (F), are shown.

Fig. S2 Secondary structures of Citrus exocortis viroid (CEVd) clones CEVd.188 (A), CEVd.189 (B) and CEVd.190 (C) as determined by integration of the SHAPE data without Mg ions into the RNAstructure 5.1 software program. TL (Terminal Left), P (Pathogenicity), C (Central), V (Variable) and TR (Terminal Right) refer to the structural domains defined in Fig. 3.

Fig. S3 RNase probing results performed on Citrus exocortis viroid clone CEVd.188. The nucleotides are highlighted according to the RNase mapping data; the green nucleotides are cleaved by RNase V1, the red ones by RNase T1 and the blue ones by RNase A. TL (Terminal Left), P (Pathogenicity), C (Central), V (Variable) and TR (Terminal Right) refer to the structural domains defined in Fig. 3.

Fig. S4 Predicted secondary structures of the Citrus viroid III variant CVd-III.072 and Citrus bent leaf viroid variant CBLVd.032. The most stable structures of CVd-III.072, as predicted by Mfold (A) and RNAstructure 5.1 (B), and of CBLVd.032, as predicted by Mfold (C) and RNAstructure 5.1 (D), are shown.

Fig. S5 Predicted secondary structures of the Hop stunt viroid variant HSVd.cit106 and Citrus viroid IV (CVd-IV) variant. The most stable structures of HSVd.cit106, as predicted by Mfold (A) and RNAstructure 5.1 (B), and of CVd-IV, as predicted by Mfold (C) and RNAstructure 5.1 (D), are shown.

Fig. S6 Secondary structures of the Citrus viroid III variant CVd-III.072 (A), Citrus bent leaf viroid variant CBLVd.032 (B), Hop stunt viroid variant HSVd.cit106 (C) and Citrus viroid IV (CVd-IV) variant (D), as determined by the integration of the SHAPE data without Mg ions into the RNAstructure 5.1 software program. TL (Terminal Left), P (Pathogenicity), C (Central), V (Variable) and TR (Terminal Right) refer to the structural domains defined in Fig. 4.

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mpp776_sm_figureS1.tif1842KSupporting info item
mpp776_sm_figureS2.tif989KSupporting info item
mpp776_sm_figureS3.tif348KSupporting info item
mpp776_sm_figureS4.tif850KSupporting info item
mpp776_sm_figureS5.tif762KSupporting info item
mpp776_sm_figureS6.tif824KSupporting info item

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