Characterization of Hibiscus Chlorotic Ringspot Virus-Derived vsiRNAs from Infected Hibiscus rosa-sinensis in China

Lots of progress have been made about pathogen system of Hibiscus rosa-sinensis and hibiscus chlorotic ringspot virus (HCRSV), however, interactions between H. rosa-sinensis and HCRSV remain largely unknown. Hereon, firstly, HCRSV infection in H. rosa-sinensis from Zhangzhou city of China was confirmed by traditional electron microscopy, modern reverse transcription polymerase chain reaction and RNA-seq methods. Secondly, sequence feature analysis showed the full-length sequence of HCRSV-ZZ was 3,909 nucleotides (nt) in length and had a similar genomic structure with other carmovirus. It contains a 5' untranslated region (UTR), followed by seven open reading frames encoding for P28, P23, P81, P8, P9, P38, and P25, and the last a 3-terminal UTR. Thirdly, HCRSV- ZZ-derived vsiRNAs were identified and characterized for the first time from disease H. rosa-sinensis through sRNA-seq to reveal interactions between pathogen ant plant host. It was shown that the majority of HCRSV-ZZ-derived vsiRNAs were 21 nt, 22 nt, and 20 nt, with 21 nt being most abundant. The 5'-terminal nucleotide of HCRSV-ZZ vsiRNAs preferred U and C. HCRSV-ZZ vsiRNAs derived predominantly (72%) from the viral genome positive-strand RNA. The distribution of HCRSV-ZZ vsiRNAs along the viral genome is generally even, with some hot spots and cold spots forming in local regions. These hot spots and cold spots could be corresponded to the regions of stem loop secondary structures forming in HCRSV-ZZ genome by nucleotide paring. Taken together, our findings certify HCRSV infection in H. rosa-sinensis and provide an insight into interaction between HCRSV and H. rosa-sinensis and contribute to the prevention and treatment of this virus.