The Identification of Viral Pathogens in a Physostegia virginiana Plant Using High-Throughput RNA Sequencing

Jinxi Dong; Yuanling Chen; Yi Xie; Mengji Cao; Shuai Fu; Jianxiang Wu

doi:10.3390/v15091972

The Identification of Viral Pathogens in a Physostegia virginiana Plant Using High-Throughput RNA Sequencing

Viruses. 2023 Sep 21;15(9):1972. doi: 10.3390/v15091972.

Authors

Jinxi Dong^{1

2}, Yuanling Chen^{1

2}, Yi Xie², Mengji Cao³, Shuai Fu⁴, Jianxiang Wu^{1

2}

Affiliations

¹ Hainan Institute, Zhejiang University, Sanya 572025, China.
² State Key Laboratory of Rice Biology, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China.
³ National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Chongqing 400712, China.
⁴ Research Center for Biological Computation, Zhejiang Lab, Hangzhou 311100, China.

Abstract

Physostegia virginiana is an important ornamental and cut-flower plant in China. Its commonly used method of clonal propagation leads to virus accumulation in this plant. However, which viruses can infect the Physostegia virginiana plant remains to be illuminated. In this work, five viral pathogens in a Physostegia virginiana plant with virus-like symptoms of yellow, shriveled, and curled leaves were identified using RNA-seq, bioinformatics, and molecular biological techniques. These techniques allowed us to identify five viruses comprising one known alfalfa mosaic virus (AMV) and four novel viruses. The novel viruses include a virus belonging to the genus Fabavirus, temporarily named Physostegia virginiana crinkle-associated virus 1 (PVCaV1); two viruses belonging to the genus Caulimovirus, temporarily named Physostegia virginiana caulimovirus 1 and 2 (PVCV1 and PVCV2); and a virus belonging to the genus Fijivirus, temporarily named Physostegia virginiana fijivirus (PVFV). The genome sequences of PVCaV1, PVCV1, and PVCV2, and the partial genome sequence of PVFV were identified. Genome organizations and genetic evolutionary relationships of all four novel viruses were analyzed. PVCaV1 has a relatively close evolutionary relationship with five analyzed fabiviruses. PVCV1 and PVCV2 have separately a closest evolutionary relationship with lamium leaf distortion-associated virus (LLDAV) and figwort mosaic virus (FMV), and PVFV has a close evolutionary relationship with the five analyzed fijiviruses. Additionally, PVCaV1 can infect Nicotiana benthamiana plants via friction inoculation. The findings enrich our understanding of Physostegia virginiana viruses and contribute to the prevention and control of Physostegia virginiana viral diseases.

Keywords: Physostegia virginiana; Physostegia virginiana caulimovirus 1; Physostegia virginiana caulimovirus 2; Physostegia virginiana crinkle-associated virus 1; Physostegia virginiana fijivirus; RNA-seq.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Alfalfa mosaic virus*
Biological Evolution
High-Throughput Nucleotide Sequencing
Nicotiana
RNA-Seq
Reoviridae*

Grants and funding

This work was supported by the National Key Research and Development Program of China (2022YFD1401200), the National Natural Science Foundation of China (31972234), and the Hainan Province Science and Technology Special Fund (ZDYF2022XDNY240).