Abstract
The sequence polymorphism and population structure of Tomato chlorotic dwarf viroid (TCDVd) (isolate Trust) and Potato tuber spindle viroid (PSTVd) (isolate FN) in tomato plants were investigated. Of the 9 and 35 TCDVd clones sequenced from 2 different TCDVd-infected plants, 2 and 4 sequence variants were identified, respectively, leading to a total of 4 sequence variants of 360 nucleotides in length. Variant I was identical to AF162131, the first TCDVd sequence to be reported, and the rest exhibited 1 to 3 nucleotide differences, all in the TR domain, from AF162131/variant I. Of the 33 and 29 PSTVd clones sequenced from 2 different PSTVd-infected plants, 8 and 9 sequence variants were found, respectively, leading to a total of 15 variants ranging in length from 356 to 359 nucleotides. The variant I was identical to EF044303, a PSTVd reported in Russia. The rest exhibited 1 to 11 nucleotide differences scattering in all five domains from EF044303/variant I. The results demonstrated for the first time that TCDVd, like many other viroids including PSTVd, exists in host plants as a collective group comprised of various sequence variants. However, in comparison to PSTVd, TCDVd is less polymorphic in tomato plants as fewer variants and lower haplotype/nucleotide diversities were observed.
Highlights
Viroids are the smallest plant pathogens that can cause a wide range of symptoms from symptomless to severe stunting, leaf/stem necrosis and foliar/fruit deformation, depending on host plant and viroid species [1]
The results demonstrated for the first time that Tomato chlorotic dwarf viroid (TCDVd), like many other viroids including Potato spindle tuber viroid (PSTVd), exists in host plants as a collective group comprised of various sequence variants
Many viroids, including PSTVd, have been suggested to propagate in their hosts as a population of similar but not identical sequences [16]. To reveal whether this is true for TCDVd, and to reveal whether there is more than one sequence variant in TCDVd isolate Trust, multiple full length cDNA clones generated from the RNA of an infected tomato plant were sequenced together with clones derived from a PSTVd-infected tomato plant
Summary
Viroids are the smallest plant pathogens that can cause a wide range of symptoms from symptomless to severe stunting, leaf/stem necrosis and foliar/fruit deformation, depending on host plant and viroid species [1]. Potato spindle tuber viroid (PSTVd), the type member of genus Pospiviroid, family Pospiviroidae, was the first viroid species to be identified [4]. It infects potato, tomato and many other solanaceous and non-solanaceous plant species and causes significant yield loss and quality degradation in potato and tomato crops [5,6,7,8]. Members of the Pospiviroidae family replicate in the nucleus by host DNA-dependent RNA polymerase II [1].
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