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. 2017 Aug 21;7:8341. doi: 10.1038/s41598-017-08823-z

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© The Author(s) 2017

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Sequence similarities between the PSTVd-sRNA binding sites of tomato and other host genomes. BLAST analyses were performed against the genomes of both potato and Nicotiana species in order to detect the presence of sequence homologies with both the chloride channel protein CLC-b-like and the RPS3a-like mRNAs of tomato as these species are the hosts of PSTVd under natural and laboratory conditions, respectively. The sequence obtained was aligned against the respective targeting vd-sRNA in order to identify any possible RISC mediated cleavage sites. The vd-sRNA targeting the chloride channel protein CLC-b-like mRNA in tomato was predicted to target (A) the potato, but not the Nicotiana species. The tomato and potato chloride channel protein CLC-b-like mRNAs have one mismatch, which is shadowed. The vd-sRNA RPS3a-like mRNA was predicted to target both the RPS3a-like (B) and the cyc07-like mRNAs (C) in potato. The same vd-sRNA can also target the RPS3a-like mRNA (D) in Nicotiana sylvestris. The arrows indicate the predicted cleavage sites.