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Ghorani S, Massumi H, Farhangi SH, Mansouri M, Heydarnejad J, Hosseinipour A. Metatranscriptome analysis of symptomatic bitter apple plants revealed mixed viral infections with a putative novel polerovirus. BMC Genomics 2024; 25:181. [PMID: 38360528 PMCID: PMC10868029 DOI: 10.1186/s12864-024-10057-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 01/27/2024] [Indexed: 02/17/2024] Open
Abstract
BACKGROUND Next-generation Sequencing (NGS) combined with bioinformatic analyses constitutes a powerful approach for identifying and characterizing previously unknown viral genomes. In this study, leaf samples from bitter apple plants (Citrullus colocynthis (L.) Schrad) exhibiting symptoms such as dwarfing, leaf crinkling, and chlorosis were collected from the southern part of Kerman province, Iran. RESULTS Putative infecting viruses were identified through de novo assembly of sequencing reads using various tools, followed by BLAST analysis. Complete genomes for Squash vein yellowing virus (SqVYV), Citrus-associated rhabdovirus (CiaRV), and a novel polerovirus-related strain termed Bitter apple aphid-borne yellows virus (BaABYV) were assembled and characterized. Additionally, a partial genome for Watermelon mosaic virus (WMV) was assembled. The genomic organization of the BaABYV was determined to be 5'-ORF0-ORF1-ORF1,2-ORF3a-ORF3-ORF3,5-ORF4-3'. Amino acid sequence identities for inferred proteins (P0 and P1, P1,2) with known poleroviruses were found to be the 90% species delineation limit, implying that BaABYV should be considered a new member of the genus Polerovirus. Recombination events were observed in the BaABYV and WMV strains; such events were not found in the CiaRV strain. CONCLUSIONS Molecular evidence from this study suggests that C. colocynthis is a reservoir host of several plant viruses. Among them, BaABYV is proposed as a new member of the genus Polerovirus. Furthermore, the CiaRV strain has been reported for the first time from Iran.
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Affiliation(s)
- Shahrbanou Ghorani
- Department of Plant Protection, College of Agriculture, Shahid Bahonar University of Kerman, Kerman, 7616914111, Iran
| | - Hossein Massumi
- Department of Plant Protection, College of Agriculture, Shahid Bahonar University of Kerman, Kerman, 7616914111, Iran.
- Research and Technology Institute of Plant Production (RTIPP), Shahid Bahonar University of Kerman, Kerman, Iran.
| | - Samin H Farhangi
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands
| | - Mehdi Mansouri
- Department of Agricultural Biotechnology, College of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Jahangir Heydarnejad
- Department of Plant Protection, College of Agriculture, Shahid Bahonar University of Kerman, Kerman, 7616914111, Iran
| | - Akbar Hosseinipour
- Department of Plant Protection, College of Agriculture, Shahid Bahonar University of Kerman, Kerman, 7616914111, Iran
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Assessment of the RNA Silencing Suppressor Activity of Protein P0 of Pepper Vein Yellows Virus 5: Uncovering Natural Variability, Relevant Motifs and Underlying Mechanism. BIOLOGY 2022; 11:biology11121801. [PMID: 36552310 PMCID: PMC9775047 DOI: 10.3390/biology11121801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/02/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022]
Abstract
Pepper vein yellows virus 5 (PeVYV-5) belongs to a group of emerging poleroviruses (family Solemoviridae) which pose a risk to pepper cultivation worldwide. Since its first detection in Spain in 2013 and the determination of the complete genome sequence of an isolate in 2018, little is known on the presence, genomic variation and molecular properties of this pathogen. As other members of genus Polerovirus, PeVYV-5 encodes a P0 protein that was predicted to act as viral suppressor of RNA silencing (VSR), one of the major antiviral defense mechanisms in plants. The results of the present work have indicated that PeVYV-5 P0 is a potent VSR, which is able to induce the degradation of Argonaute (AGO) endonucleases, the main effectors of RNA silencing. New viral isolates have been identified in samples collected in 2020-2021 and sequencing of their P0 gene has revealed limited heterogeneity, suggesting that the protein is under negative selection. Analysis of natural and engineered P0 variants has pinpointed distinct protein motifs as critical for the VSR role. Moreover, a positive correlation between the VSR activity of the protein and its capability to promote AGO degradation could be established, supporting that such activity essentially relies on the clearance of core components of the RNA silencing machinery.
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Zhao K, Yin Y, Hua M, Wang S, Mo X, Yuan E, Zheng H, Lin L, Chen H, Lu Y, Chen J, Peng J, Yan F. Pod pepper vein yellows virus, a new recombinant polerovirus infecting Capsicum frutescens in Yunnan province, China. Virol J 2021; 18:42. [PMID: 33622354 PMCID: PMC7901092 DOI: 10.1186/s12985-021-01511-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 02/08/2021] [Indexed: 12/02/2022] Open
Abstract
Pepper vein yellows viruses (PeVYV) are phloem-restricted viruses in the genus Polerovirus, family Luteoviridae. Typical viral symptoms of PeVYV including interveinal yellowing of leaves and upward leaf curling were observed in pod pepper plants (Capsicum frutescens) growing in Wenshan city, Yunnan province, China. The complete genome sequence of a virus from a sample of these plants was determined by next-generation sequencing and RT-PCR. Pod pepper vein yellows virus (PoPeVYV) (MT188667) has a genome of 6015 nucleotides, and the characteristic genome organization of a member of the genus Polerovirus. In the 5′ half of its genome (encoding P0 to P4), PoPeVYV is most similar (93.1% nt identity) to PeVYV-3 (Pepper vein yellows virus 3) (KP326573) but diverges greatly in the 3′-part encoding P5, where it is most similar (91.7% nt identity) to tobacco vein distorting virus (TVDV, EF529624) suggesting a recombinant origin. Recombination analysis predicted a single recombination event affecting nucleotide positions 4126 to 5192 nt, with PeVYV-3 as the major parent but with the region 4126–5192 nt derived from TVDV as the minor parent. A full-length clone of PoPeVYV was constructed and shown to be infectious in C. frutescens by RT-PCR and the presence of icosahedral viral particles.
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Affiliation(s)
- Kuangjie Zhao
- State Key Laboratory for Managing Biotic and Chemical Threats To the Quality and Safety of Agroproducts, Institute of Plant Virology, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Yueyan Yin
- Institute of Alpine Economic Plants, Yunnan Academy of Agricultural Sciences, Lijiang, 674100, Yunnan, China.,College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Mengying Hua
- State Key Laboratory for Managing Biotic and Chemical Threats To the Quality and Safety of Agroproducts, Institute of Plant Virology, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Shaoxiang Wang
- Wenshan Academy of Agricultural Sciences, Wenshan, 663000, Yunnan, China
| | - Xiaohan Mo
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, Yunnan, China
| | - Enping Yuan
- Wenshan Academy of Agricultural Sciences, Wenshan, 663000, Yunnan, China
| | - Hongying Zheng
- State Key Laboratory for Managing Biotic and Chemical Threats To the Quality and Safety of Agroproducts, Institute of Plant Virology, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Lin Lin
- State Key Laboratory for Managing Biotic and Chemical Threats To the Quality and Safety of Agroproducts, Institute of Plant Virology, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Hairu Chen
- College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Yuwen Lu
- State Key Laboratory for Managing Biotic and Chemical Threats To the Quality and Safety of Agroproducts, Institute of Plant Virology, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Jianping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats To the Quality and Safety of Agroproducts, Institute of Plant Virology, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Jiejun Peng
- State Key Laboratory for Managing Biotic and Chemical Threats To the Quality and Safety of Agroproducts, Institute of Plant Virology, Ningbo University, Ningbo, 315211, Zhejiang, China.
| | - Fei Yan
- State Key Laboratory for Managing Biotic and Chemical Threats To the Quality and Safety of Agroproducts, Institute of Plant Virology, Ningbo University, Ningbo, 315211, Zhejiang, China.
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