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Li T, Ye ZX, Huang YL, Chen JP, Zhang CX, Li JM. Complete genome sequence of a novel amalgavirus in sponge gourd, Luffa cylindrica. Arch Virol 2024; 169:160. [PMID: 38981875 DOI: 10.1007/s00705-024-06094-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 06/17/2024] [Indexed: 07/11/2024]
Abstract
A novel monopartite dsRNA virus, tentatively named "sponge gourd amalgavirus 1" (SGAV1), was discovered by high-throughput sequencing in sponge gourd (Luffa cylindrica) displaying mosaic symptoms in Jiashan County, Zhejiang Province, China. The genome of SGAV1 is 3,447 nucleotides in length and contains partially overlapping open reading frames (ORFs) encoding a putative replication factory matrix-like protein and a fusion protein, respectively. The fusion protein of SGAV1 shares 57.07% identity with the homologous protein of salvia miltiorrhiza amalgavirus 1 (accession no. DAZ91057.1). Phylogenetic analysis based on the RNA-dependent RNA polymerase (RdRp) protein suggests that SGAV1 belongs to the genus Amalgavirus of the family Amalgaviridae. Moreover, analysis of SGAV1-derived small interfering RNAs indicated that SGAV1 was actively replicating in the host plant. Semi-quantitative RT-PCR showed higher levels of SGAV1 expression in leaves than in flowers and fruits. This is the first report of a novel amalgavirus found in sponge gourd in China.
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Affiliation(s)
- Ting Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
- College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, China
| | - Zhuang-Xin Ye
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Yao-Liang Huang
- Jiashan Agro-Tech Extension and Service Center, Jiashan, 314199, China
| | - Jian-Ping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
- College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, China
| | - Chuan-Xi Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Jun-Min Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China.
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Yuan Z, Li Z, Lu Y, Cao M, Hong N, Wang G, Cai L. Molecular characterization of a novel amalgavirus infecting lilium spp. in China. Arch Virol 2023; 168:181. [PMID: 37314504 DOI: 10.1007/s00705-023-05806-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 04/26/2023] [Indexed: 06/15/2023]
Abstract
A novel plant virus with a double-stranded (ds) RNA genome was detected in Lilium spp. in China by high-throughput sequencing and tentatively named "lily amalgavirus 2" (LAV2). The genomic RNA of LAV2 is 3432 nucleotides (nt) in length and contains two open reading frames (ORFs) that putatively encode a '1 + 2' fusion protein of 1053 amino acids (aa), generated by a '+1' programmed ribosomal frameshift (PRF). ORF1 encodes a putative 386-aa protein of unknown function, and ORF2 overlaps ORF1 by 350 nt and encodes a putative 783-aa protein with conserved RNA-dependent RNA polymerase (RdRp) motifs. The '+1' ribosomal frameshifting motif, UUU_CGN, which is highly conserved among amalgaviruses, is also found in LAV2. Sequence analysis showed that the complete genome shared 46.04%-51.59% nucleotide sequence identity with those of members of the genus Amalgavirus and had the most similarity (51.59% sequence identity) to lily amalgavirus 1 (accession no. OM782323). Phylogenetic analysis based on RdRp amino acid sequences showed that LAV2 clustered with members of the genus Amalgavirus. Overall, our data suggest that LAV2 is a new member of the genus Amalgavirus.
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Affiliation(s)
- Zhihao Yuan
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, 430070, Wuhan, China
| | - Zhenfeng Li
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, 430070, Wuhan, China
| | - Yuexia Lu
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, 430070, Wuhan, China
| | - Mengji Cao
- National Citrus Engineering Research Center, Southwest University, 400712, Chongqing, China
| | - Ni Hong
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, 430070, Wuhan, China
| | - Guoping Wang
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, 430070, Wuhan, China
| | - Li Cai
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, 430070, Wuhan, China.
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Sidharthan VK, Rajeswari V, Vanamala G, Baranwal VK. Revisiting the amalgaviral landscapes in plant transcriptomes expands the host range of plant amalgaviruses. Virology 2022; 577:65-73. [PMID: 36308887 DOI: 10.1016/j.virol.2022.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 10/09/2022] [Accepted: 10/16/2022] [Indexed: 11/19/2022]
Abstract
Plant amalgaviruses are monopartite, double-stranded RNA viruses, capable of vertical transmission through seeds. An attempt to revisit plant transcriptome-assembled contigs for amalgaviral sequences identified 40 putative novel amalgaviruses in 35 plant species, nearly doubling the number of plant amalgaviruses. Of the 35 plant species, 33 are reported to host amalgaviruses for the first time, including a pteridophytic and two gymnospermic species. Coding-complete genomes of all identified viruses were recovered and the putative +1 programmed ribosomal frameshift (PRF) sites were determined. Genomes of 35 identified amalgaviruses contained the conserved +1 PRF motif 'UUU_CGN', while variant versions were predicted in five genomes. Phylogenetic analysis grouped pteridophyte- and gymnosperm-infecting amalgaviruses together in divergent sub-clades while few of the related angiosperm-infecting amalgaviruses infect members of the same plant family, reiterating the co-evolution of plant amalgaviruses and their hosts. The current study paves way for further studies on understanding biological properties of identified viruses.
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Affiliation(s)
- V Kavi Sidharthan
- Division of Genetics and Tree Improvement, Institute of Forest Biodiversity (ICFRE), Hyderabad, India.
| | - V Rajeswari
- Department of Crop Physiology, Tamil Nadu Agricultural University, Coimbatore, India
| | - Gayatri Vanamala
- Division of Genetics and Tree Improvement, Institute of Forest Biodiversity (ICFRE), Hyderabad, India
| | - V K Baranwal
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India.
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