Interference between variants of peach latent mosaic viroid reveals novel features of its fitness landscape: implications for detection

[EN] Natural populations of peach latent mosaic viroid (PLMVd) are complex mixtures of variants. During routine testing, TaqMan rtRT-PCR and RNA gel-blot hybridization produced discordant results with some PLMVd isolates. Analysis of the corresponding populations showed that they were exclusively composed of variants (of class II) with a structural domain different from that of the reference and many other variants (of class I) targeted by the TaqMan rtRT-PCR probe. Bioassays in peach revealed that a representative PLMVd variant of class II replicated without symptoms, generated a progeny with low nucleotide diversity, and, intriguingly, outcompeted a representative symptomatic variant of class I when co-inoculated in equimolecular amounts. A number of informative positions associated with the higher fitness of variants of class II have been identified, and novel sets of primers and probes for universal or specific TaqMan rtRT-PCR detection of PLMVd variants have been designed and tested.We thank A. Ahuir for excellent technical assistance and Dr. Francesco Di Serio for suggestions. This work was supported by grant BFU2014-56812-P (to R.F.) from Ministerio de Economia y Competitividad (MINECO) of Spain. P.S. was the recipient of a postdoctoral contract from MINECO and E. Bertolini of an INIA-CCA2011-2016 contract also from MINECO.Serra Alfonso, P.; Bertolini, E.; Martinez, MC.; Cambra, M.; Flores Pedauye, R. (2017). Interference between variants of peach latent mosaic viroid reveals novel features of its fitness landscape: implications for detection. Scientific Reports. 7. https://doi.org/10.1038/srep42825S7Diener, T. O. Discovering viroids - a personal perspective. Nat. Rev. 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Transmission of ‘Candidatus Liberibacter solanacearum’ by Bactericera trigonica Hodkinson to vegetable hosts

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