Identification and Characterization of Two Novel Noda-like Viruses from Rice Plants Showing the Dwarfing Symptom

Xie, Yi; Fu, Shuai; Xie, Li; Wang, Yaqin; Cao, Mengji; Zhou, Xueping; Wu, Jianxiang

doi:10.3390/v14061159

Cited by 3 publications

(2 citation statements)

References 71 publications

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“…1a). To identify the potential viruses in collected leaves, RNA-seq was performed as described previously [1,6,7]. Brie y, the EASYspin Plus Complex Plant RNA Kit (Aidlab Biotech, Beijing, China) was used to extract total RNA from the sampled leaf tissues.…”

Section: Mainmentioning

confidence: 99%

Molecular characterization of a novel chlorotic leaf curl-associated foveavirus infecting prune trees

Zheng

Han

Gong

et al. 2022

Preprint

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The Prune tree (Prunus mume) is widely distributed in East Asian countries for fruit, medicinal herbs, or ornamental purposes for more than 2000 years. High-throughput sequencing in prune tree leaves showing chlorosis and leaf curl symptoms sampled from the China National Botanical Garden revealed the presence of a putative novel virus belonging to the genus Foveavirus, the family Betaflexiviridae. We cloned the completion genome of this new virus and named this virus as prune tree chlorotic leaf curl-associated virus (PTCLCaV). The genome of PTCLCaV is a 9 034 nucleotide (nt) positive-sense, single strand RNA, excluding its 3’ poly (A) tail, and contains five open reading frames (ORFs). ORF1 encodes a putative viral replication-associated protein (Rep), and ORFs 2, 3, and 4 encode the triple gene block (TGB) proteins. ORF5 encodes the capsid protein (CP). Our phylogenetic analysis demonstrated that PTCLCaV is evolutionarily related to members from the genus Foveavirus of the family Betaflexiviridae. Based on sequence identity and phylogenetic analysis, PTCLCaV represents a new species of the genus Foveavirus in the family Betaflexiviridae.

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Section: Mainmentioning

confidence: 99%

Molecular characterization of a novel chlorotic leaf curl-associated foveavirus infecting prune trees

Zheng

Han

Gong

et al. 2022

Preprint

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“…For example, its throughput is very high, only a small number of samples are required, the genomic characteristic of the virus is not necessary to be known in advance, and the detection accuracy is up to a single base [ 7 ]. Using the RNA-seq technique, numerous new viruses were identified [ 8 , 9 , 10 , 11 ].…”

Section: Introductionmentioning

confidence: 99%

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

Dong,

Chen,

Xie

et al. 2023

Viruses

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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.

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Discovery and Characterization of a Novel Umbravirus from Paederia scandens Plants Showing Leaf Chlorosis and Yellowing Symptoms

Zheng

Xie

et al. 2022

Viruses

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Umbraviruses are a special class of plant viruses that do not encode any viral structural proteins. Here, a novel umbravirus that has been tentatively named Paederia scandens chlorosis yellow virus (PSCYV) was discovered through RNA-seq in Paederia scandens plants showing leaf chlorosis and yellowing symptoms. The PSCYV genome is a 4301 nt positive-sense, single strand RNA that contains four open reading frames (ORFs), i.e., ORF1–4, that encode P1–P4 proteins, respectively. Together, ORF1 and ORF2 are predicted to encode an additional protein, RdRp, through a −1 frameshift mechanism. The P3 protein encoded by ORF3 was predicted to be the viral long-distance movement protein. P4 was determined to function as the viral cell-to-cell movement protein (MP) and transcriptional gene silencing (TGS) suppressor. Both P1 and RdRp function as weak post-transcriptional gene silencing (PTGS) suppressors of PSCYV. The PVX-expression system indicated that all viral proteins may be symptom determinants of PSCYV. Phylogenetic analysis indicated that PSCYV is evolutionarily related to members of the genus Umbravirus in the family Tombusviridae. Furthermore, a cDNA infectious clone of PSCYV was successfully constructed and used to prove that PSCYV can infect both Paederia scandens and Nicotiana benthamiana plants through mechanical inoculation, causing leaf chlorosis and yellowing symptoms. These findings have broadened our understanding of umbraviruses and their host range.

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Identification and Characterization of Two Novel Noda-like Viruses from Rice Plants Showing the Dwarfing Symptom

Cited by 3 publications

References 71 publications

Molecular characterization of a novel chlorotic leaf curl-associated foveavirus infecting prune trees

Molecular characterization of a novel chlorotic leaf curl-associated foveavirus infecting prune trees

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

Discovery and Characterization of a Novel Umbravirus from Paederia scandens Plants Showing Leaf Chlorosis and Yellowing Symptoms

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