Nucleotide sequence of the original Brazilian isolate of coleus yellow viroid from Solenostemon scutellarioides and infectivity of its complementary DNA

Infectious cDNA clones of four viroids in Coleus blumei and molecular characterization of their progeny

Four viroid species infecting Coleus blumei, named Coleus blumei viroid 1-4 (CbVd-1-CbVd-4), and two tentative new viroid species, named CbVd-5 and CbVd-6, have been characterized, for two of which (CbVd-5 and CbVd-6, first reported in 2009), there is no established bioassay. Here, infectious clones were used as inoculums sources and the biological properties of CbVd-1, -3, -5 and -6 were assessed. When dimeric CbVd (+) RNAs synthesized in vitro were bioassayed, the first detection time for the four CbVds was different, ranging from 45 to 300 days. In addition, we confirmed that CbVd-5 and CbVd-6 can be transmitted via seeds. Molecular characterization of their progeny from slash-inoculated plants one year after inoculation demonstrated that the genetic diversity of CbVd populations may depend on the infected coleus plants and on the viroid genotype.

Identification and characterization of a new coleviroid (CbVd-5)

A viroid-like RNA was detected from coleus (Coleus blumei) in China. It consisted of 274 nucleotides and had 66% sequence identity with a member of the closest known viroid species. The predicted secondary structure is rod-shaped with extensive base pairing, and it has the conserved region characteristic of the genus Coleviroid. Two terminal sequences that are highly conserved among some members of the genus were also identified. The viroid-like RNA was successfully transmitted to coleus by slash-inoculation. This viroid was identified as a new member of the genus Coleviroid, and we tentatively propose the name Coleus blumei viroid 5 (CbVd-5).

A new sequence variant of Coleus blumei viroid 1 from the Coleus blumei cultivar "Rainbow Gold'

A viroid was isolated from symptomless Coleus blumei cultivar (cv.) 'Rainbow Gold' plants using the bidirectional PAGE method for analysis of small circular RNA molecules. The viriod was transmitted to viroid-free plants of Coleus blumei cv. 'Scarlet Dragonfly' by mechanical inoculation. Cloning and sequencing revealed that the viriod from the Coleus cv. 'Rainbow Gold' is closely related to the Coleus blumei viriod 1-BvA (CbVd 1-BvA) isolated from the Coleus cv. 'Bienvenue'. Therefore, new viroid sequence variant has been named Coleus blumei viriod 1-RG (CbVd 1-RG). Coleus blumei viriod 1-RG consists of 251 nucleotides, 140 G + C, 111 A + U with a GC content of 55.4%. The most stable rod-like secondary structure of this viroid has 53 G:C, 29 A:U and 5 G:U base pairs with a minimum free energy (at 25 degrees C) of -81.2 kcal/mol (-339.4 kJ/mol). The right terminal domain shows a high sequence similarity to the corresponding domain of hop latent viroid (HLVd).

A new sequence variant of Coleus blumei viroid 3 from the Coleus blumei cultivar 'Fairway Ruby'

A viroid was isolated from symptomless Coleus blumei cultivar (cv) 'Fairway Ruby' plants using the bidirectional PAGE method for analysis of small circular RNA molecules. The viroid was transmitted to viroid-free plants of Coleus blumei cv. 'Scarlet Dragonfly' by mechanical inoculation. Cloning and sequencing revealed that the viroid from the Coleus cv. 'Fairway Ruby' is closely related to the Coleus blumei viroid 3-Bv (CbVd 3-Bv) isolated from the Coleus cv. 'Bienvenue'. Therefore, the new viroid sequence variant has been named Coleus blumei viroid 3-FR (CbVd 3-FR). Coleus blumei viroid 3-FR consists of 364 nucleotides, 202 G + C, 162 A + U with a GC content of 55.5%. The most stable rod-like secondary structure of this viroid has 82 G:C, 50 A:U and 10 G:U base pairs with a minimum free energy of -670.5 kJ/mol (-160.4 kcal/mol). Due to mutations that increase the stability of the rod-like secondary structure, CbVd 3-FR has a lower minimum free energy than CbVd 3-Bv (-598.2 kJ/mol; -143.1 kcal/mol). A base-exchange in the upper strand of the central domain of CbVd 3-FR may stabilize the basal helix of hairpin I.

A viroid from Solanum pseudocapsicum closely related to the tomato apical stunt viroid

A viroid was isolated from symptomless Solanum pseudocapsicum cultivar (cv) 'New Patterson' plants using the bidirectional PAGE method for analysis of small circular RNA molecules. The viroid was transmitted to tomato by mechanical inoculation. Infected tomato plants developed symptoms similar to those caused by potato spindle tuber viroid (PSTVd). Cloning and sequencing revealed that the viroid from Solanum pseudocapsicum is closely related to the tomato apical stunt viroid (TASVd). Therefore, the new viroid sequence variant has been named TASVd-S. The circular RNA of TASVd-S consists of 360 nucleotides which can potentially form a rod-like structure with a high degree of base-pairing like all the other known viroids. The nucleotide composition is 99 G, 72 A, 101 C and 88 U, corresponding to 200 G + C, 160 A + U with a GC content of 55.6%. In total 71% of the residues are base-paired and the basepaired residues consist of 73 G:C (57%), 43 A:U (34%) and 11 G:U (9%) base pairs. The most stable rod-like secondary structure of this viroid has 80 G:C, 39 A:U and 11 G:U base pairs with a minimum free energy of -147.5 kcal/mol (-616.6 kJ/mol). The sequence similarity of the left terminal (T1) domain of TASVd-S and the T1 domain of tomato planta macho viroid (TPMVd) is higher than the sequence similarity of these domains of TASVd-S and TASV-d.

Compilation and analysis of viroid and viroid-like RNA sequences

We have created a catalogue comprising all viroid and viroid-like RNA sequences which to our knowledge have been either published or were available from on-line sequence libraries as of October 1, 1995. In the development of this catalogue nomenclature ambiguities were removed, the likely ancestral sequence of most species was determined and the most stable secondary structures of these sequences were predicted using the MulFold package. Only viroids of PSTVd-type possessed a rod-like secondary structure, while most other viroids adopted branched secondary structures. Several viroids have predicted secondary structures that include either a Y or cruciform structure reminiscent of the tRNA-like end of virus genomes at an extremity. However, it remains unknown whether or not these predicted structures are adopted in solution, and if they serve a particular function in vivo. Additional information such as the position of the self-catalytic domains are included in the catalogue. An analysis of the data compilated in the catalogue is included. The catalogue will be available on the world wide web (http://www.callistro.si.usherb.ca/jpperra), on computer disk and in printed form. It should provide an excellent reference point for further studies.

A rapid and sensitive dot-blot hybridization assay for the detection of citrus exocortis viroid in Citrus medica with digoxigenin-labelled RNA probes

A rapid and sensitive dot-blot hybridization assay using in vitro-transcribed digoxigenin-labelled RNA probes (riboprobes) was developed aiming at detection of citrus exocortis viroid (CEVd) in crude sap of infected Citrus medica plants. The protocol includes a very quick and simple preparation of RNA extracts from samples using a denaturation step with formaldehyde. From our results, the employment of this step is highly recommended because the hybridization signals in formaldehyde-denatured samples were significantly stronger when compared with that of extracts without formaldehyde treatment. The assay was found to be sensitive enough to detect 0.1 ng of purified CEVd RNA and was able to detect viroid in 0.2 mg of symptomatic Citrus medica leaves. The use of riboprobes also allowed hybridization under high temperature conditions, avoiding non-specific background.