Plant Virome Analysis by the Deep Sequencing of Small RNAs of Fritillaria thunbergii var. chekiangensis and the Rapid Identification of Viruses

Abstract

Thunberg fritillary (<i>Fritillaria thunbergii</i>), a perennial used in traditional Chinese herbal medicine, is a members of the family <i>Liliaceae</i>. The degeneration of germplasm is a severe problem in the production of <i>Fritillaria thunbergii</i> var. <i>chekiangensis</i>. However, no information about viral infections of <i>F. thunbergii</i> var. <i>chekiangensis</i> has been reported. In this study, we sequenced the small RNAs of <i>F. thunbergii</i> var. <i>chekiangensis</i> from leaves and bulbs, and viruses were identified using a phylogenetic analysis and BLAST search for sequence. In addition, multiplex reverse transcriptase-polymerase chain reaction (RT-PCR) was used to rapidly detect viruses in this variety. Our study first reported that five viruses infected <i>F. thunbergii</i> var. <i>chekiangensis</i>. Among them, fritillary virus Y (FVY), lily mottle virus (LMoV), Thunberg fritillary mosaic virus (TFMV), and hop yellow virus (HYV) had been reported in <i>F. thunbergii</i>, while apple stem grooving virus was first reported in the genus <i>Fritillaria</i>. A multiplex RT-PCR method was developed to rapidly test the four viruses FVY, LMoV, TFMV, and HYV in <i>F. thunbergii</i> var. <i>chekiangensis</i>. Our results provide a better understanding of the infection of <i>F. thunbergii</i> var. <i>chekiangensis</i> by viruses and a basic reference for the better design of suitable control measures.