The Bias in Small RNA Profiles Between Symptomless Dendrobium and Severe Symptom Ascocenda Orchids Infected Long-Term with Cymbidium Mosaic Virus

Abstract

Perennial orchids worldwide are frequently infected with Cymbidium mosaic virus (CymMV). To date, no studies have described non-coding small RNA (sRNA) responses in the CymMV long-term-infected orchids. In this study, sRNA profiles of microRNAs (miRNA) and small virus-derived interfering RNAs (siRNA) in symptomless, long-term CymMV-infected Dendrobium and severe symptom, long-term CymMV-infected Ascocenda were identified in four sRNA libraries of virus-free and CymMV-infected orchids by Illumina high-throughput sequencing. The miRNA analysis revealed that the infected orchids had unique sRNA profiles that differed in size distribution, specially the presence of 21 nt sequences in severe symptom Ascocenda. Gel blot analysis showed a change in the miR528 expression which was at high level in virus free Ascocenda, on the other hand, only detected at low level in severe symptom Ascocenda. This expression alteration was also detected with the miR156 expression level in Dendrobium. Moreover, the characterization in polarity of CymMV-derived siRNAs in both infected orchids demonstrated that antisense polarity siRNAs accumulated in severe symptom Ascocenda, and the symptomless Dendrobium contained more sense polarity siRNAs. Here, we showed that miRNA expression was altered after long-term CymMV infection. Furthermore, a different pattern of siRNAs was observed between two orchid genera infected with the same virus and depended on the symptom severity.