High-throughput sequencing reveals the presence of novel and known viruses in diseased Paris yunnanensis

Authors: LAN, PINGXIU - Yunnan Agricultural University; HE, PENG - Yunnan Agricultural University; YANG, JIE - Yunnan Agricultural University; CAM, MENGJI - Southwest University; ZHOU, GUOHUA - Yunnan Agricultural University; CHEN, XIAOJIAO - Yunnan Agricultural University; WEI, TAIYUN - Yunnan Agricultural University; Li, Ruhui; LI, FAN - Yunnan Agricultural University

Submitted to: Frontiers in Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/21/2022
Publication Date: 12/14/2022
Citation: Lan, P., He, P., Yang, J., Cam, M., Zhou, G., Chen, X., Wei, T., Li, R., Li, F. 2022. High-throughput sequencing reveals the presence of novel and known viruses in diseased Paris yunnanensis. Frontiers in Microbiology. https://doi.org/10.3389/fmicb.2022.1045750.
DOI: https://doi.org/10.3389/fmicb.2022.1045750

Interpretive Summary: Dai chonglu (Paris yunnanensis) is an economically valuable medicinal herb of the genus Paris in the family Melanthiaceae. Its rhizome is an important component of human medicines in China. Due to its slow growth and overharvesting, the population of wild resources of the plant is endangered. Increased pharmaceutical uses have stimulated managed cultivation and production of the plant since 1980s, which has also introduced numerous disease problems that cause yield losses. In this study, eight viruses were found in diseased samples of P. yunnanensis from farms in Yunnan province, China. Among them, three are new viruses and two are known viruses but reported in this plant for the first time. The genetic information for these five viruses were determined and used to develop molecular detection methods. A virus survey of the fields in four counties of the province showed that two of the viruses (one new and one known) are commonplace. This study provides the information necessary to classify the viruses, and to develop detection methods for virus disease management in Paris production.

Technical Abstract: Viral diseases of Paris yunnanensis have become a serious problem in cultivation of this important medicinal plant. In this study, eight viruses were identified in plants of various symptoms by high-throughput sequencing (HTS). These viruses include three novel viruses (two of the genus Potyvirus and one of genus Nepovirus), Hippeastrum chlorotic ringspot virus (HCRV, genus Orthotospovirus) and Lychnis mottle virus (LycMoV, genus Stralarivirus), Paris mosaic necrosis virus (PMNV, genus Potyvirus) and pepper mild mottle virus (PMMoV, genus Tobamovirus). The presence of all viruses was confirmed by RT-PCR using virus-specific primers, respectively. Complete genome sequences of three novel viruses were determined. Sequence analyses showed that they shared the highest amino acid (aa) sequence identities of 53-57% to known potyviruses and 53% to a known nepovirus, respectively. Phylogenetic analyses support that the three viruses are novel members of their corresponding genera. These viruses were tentatively named Paris mosaic associated potyvirus 1 (PMaPV-1), PMaPV-2 and Paris nepovirus 1 (PNV-1), respectively. Nearly complete genome sequences of HCRV and LycMoV were also determined, and they had 97% aa sequence identities with type species at replicase. The two viruses are first reported in Paris spp. A total of 123 field samples collected from four counties in Yunnan were tested by RT-PCR for the determination of infection rate and distribution of each of the eight viruses. Results showed that nearly half of the samples tested positive for at least one of the eight viruses. Two potyviruses, PMNV and PMaPV-1 were predominant in the fields, while other viruses occurred in low rates and/or had limited distribution. This study insight into the virome infecting Paris spp. and provided valuable information for diagnosis and control of viral diseases in P. Yunnanensis.