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Viruses 2012, 4(6), 940-953; doi:10.3390/v4060940
Article

Analysis of Sequence Polymorphism and Population Structure of Tomato chlorotic dwarf viroid and Potato spindle tuber viroid in Viroid-Infected Tomato Plants

Received: 11 April 2012; in revised form: 15 May 2012 / Accepted: 30 May 2012 / Published: 5 June 2012
(This article belongs to the Special Issue Plant Viruses)
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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.
Keywords: TCDVd; PSTVd; sequence variants; polymorphism; population TCDVd; PSTVd; sequence variants; polymorphism; population
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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MDPI and ACS Style

Nie, X. Analysis of Sequence Polymorphism and Population Structure of Tomato chlorotic dwarf viroid and Potato spindle tuber viroid in Viroid-Infected Tomato Plants. Viruses 2012, 4, 940-953.

AMA Style

Nie X. Analysis of Sequence Polymorphism and Population Structure of Tomato chlorotic dwarf viroid and Potato spindle tuber viroid in Viroid-Infected Tomato Plants. Viruses. 2012; 4(6):940-953.

Chicago/Turabian Style

Nie, Xianzhou. 2012. "Analysis of Sequence Polymorphism and Population Structure of Tomato chlorotic dwarf viroid and Potato spindle tuber viroid in Viroid-Infected Tomato Plants." Viruses 4, no. 6: 940-953.


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