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.