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.