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High-Throughput Sequencing Analysis of Small RNAs Derived from Coleus Blumei Viroids

Beijing Research Center for Agricultural Standards and Testing, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100097, China
Authors to whom correspondence should be addressed.
Viruses 2019, 11(7), 619;
Received: 21 May 2019 / Revised: 24 June 2019 / Accepted: 2 July 2019 / Published: 5 July 2019
(This article belongs to the Special Issue Viroid-2018: International Conference on Viroids and Viroid-Like RNAs)
PDF [1495 KB, uploaded 5 July 2019]


Characterization of viroid-derived small RNAs (vd-sRNAs) is important to understand viroid–host interactions; however, vd-sRNAs belonging to the genus Coleviroid are yet to be identified and characterized. Herein, we used coleus plants singly infected with coleus blumei viroid (CbVd)-1, -5, or -6 and doubly infected with CbVd-1 and -5 to identify and analyze their vd-sRNAs. We found sense and antisense vd-sRNAs for CbVd-1, -5 and -6, and 22-nt vd-sRNAs were the most abundant; moreover, the 5′-terminal nucleotides (nts) of CbVd-1, -5, and -6 were biased toward U and C, and sRNAs derived from these three viroids were unevenly distributed along their genomes. We also noted that CbVd-5 and -6 share a fragment that forms the right half of the rod-like secondary structure of these viroids, which implied that they generated almost the same type of vd-sRNAs. This finding indicated that vd-sRNA biogenesis is mainly determined by the primary sequence of their substrates. More importantly, we found two complementary vd-sRNAs (22 nt) that were generated from the central conserved region (CCR) of these three viroids, suggesting an important role of CCR in vd-sRNA biogenesis. In conclusion, our results provide novel insight into the biogenesis of vd-sRNAs and the biological roles of CCR. View Full-Text
Keywords: viroid; small RNA; sRNA; coleus blumei; high-throughput sequencing viroid; small RNA; sRNA; coleus blumei; high-throughput sequencing

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Jiang, D.-M.; Wang, M.; Li, S.-F.; Zhang, Z.-X. High-Throughput Sequencing Analysis of Small RNAs Derived from Coleus Blumei Viroids. Viruses 2019, 11, 619.

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