|
1
|
He C, Wang L, Li Y, Zhou K, Zhao K, Chen D, Li J, Song H, Tu M. Loquat ( Eriobotrya japonica) Is a New Natural Host of Tomato Mosaic Virus and Citrus Exocortis Viroid. PLANTS (BASEL, SWITZERLAND) 2024; 13:1965. [PMID: 39065492 PMCID: PMC11280522 DOI: 10.3390/plants13141965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 07/15/2024] [Accepted: 07/16/2024] [Indexed: 07/28/2024]
Abstract
Loquat leaves exhibiting obvious yellowing, blistering, mosaic, leaf upward cupping, crinkle, and leaf narrowing were identified in Panzhihua City, Sichuan Province, China. High-throughput sequencing (HTS) with the ribo-depleted cDNA library was employed to identify the virome in the loquat samples; only tomato mosaic virus (ToMV) and citrus exocortis viroid (CEVd) were identified in the transcriptome data. The complete genome sequence of ToMV and CEVd were obtained from the loquat leaves. The full-length genome of the ToMV-loquat is 6376 nt and comprises four open reading frames (ORFs) encoding 183 kDa protein, RNA-dependent RNA polymerase (RdRp), movement protein (MP), and coat protein (CP), respectively. A pairwise identity analysis showed that the complete sequence of the ToMV-loquat had a nucleotide identity between 98.5 and 99.3% with other ToMV isolates. A phylogenetic analysis indicated that ToMV-loquat was more closely related to ToMV-IFA9 (GenBank No. ON156781). A CEVd sequence with 361 nt in length was amplified based on the HTS contigs, sequence alignment indicated CEVd-loquat had the highest identity with the strain of CEVd-Balad (GenBank No. PP869624), phylogenetic analysis showed that CEVd-loquat was more closely related to CEVd-lettuce (GenBank No. ON993891). This significant discovery marks the first documentation and characterization of ToMV and CEVd infecting loquat plants, shedding light on potential threats to loquat cultivation and providing insights for disease management strategies.
Collapse
Affiliation(s)
- Chengyong He
- Institute of Horticulture, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (C.H.); (L.W.); (Y.L.); (K.Z.); (K.Z.); (D.C.); (J.L.); (H.S.)
- Key Laboratory of Horticultural Crop Biology and Germplasm Creation in Southwest China, Ministry of Agriculture and Rural Affairs, Chengdu 610066, China
| | - Lingli Wang
- Institute of Horticulture, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (C.H.); (L.W.); (Y.L.); (K.Z.); (K.Z.); (D.C.); (J.L.); (H.S.)
- Key Laboratory of Horticultural Crop Biology and Germplasm Creation in Southwest China, Ministry of Agriculture and Rural Affairs, Chengdu 610066, China
| | - Yarui Li
- Institute of Horticulture, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (C.H.); (L.W.); (Y.L.); (K.Z.); (K.Z.); (D.C.); (J.L.); (H.S.)
- Key Laboratory of Horticultural Crop Biology and Germplasm Creation in Southwest China, Ministry of Agriculture and Rural Affairs, Chengdu 610066, China
| | - Kangyu Zhou
- Institute of Horticulture, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (C.H.); (L.W.); (Y.L.); (K.Z.); (K.Z.); (D.C.); (J.L.); (H.S.)
- Key Laboratory of Horticultural Crop Biology and Germplasm Creation in Southwest China, Ministry of Agriculture and Rural Affairs, Chengdu 610066, China
- College of Horticulture, Anhui Agricultural University, Hefei 230036, China
| | - Ke Zhao
- Institute of Horticulture, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (C.H.); (L.W.); (Y.L.); (K.Z.); (K.Z.); (D.C.); (J.L.); (H.S.)
- Key Laboratory of Horticultural Crop Biology and Germplasm Creation in Southwest China, Ministry of Agriculture and Rural Affairs, Chengdu 610066, China
| | - Dong Chen
- Institute of Horticulture, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (C.H.); (L.W.); (Y.L.); (K.Z.); (K.Z.); (D.C.); (J.L.); (H.S.)
- Key Laboratory of Horticultural Crop Biology and Germplasm Creation in Southwest China, Ministry of Agriculture and Rural Affairs, Chengdu 610066, China
| | - Jing Li
- Institute of Horticulture, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (C.H.); (L.W.); (Y.L.); (K.Z.); (K.Z.); (D.C.); (J.L.); (H.S.)
- Key Laboratory of Horticultural Crop Biology and Germplasm Creation in Southwest China, Ministry of Agriculture and Rural Affairs, Chengdu 610066, China
| | - Haiyan Song
- Institute of Horticulture, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (C.H.); (L.W.); (Y.L.); (K.Z.); (K.Z.); (D.C.); (J.L.); (H.S.)
- Key Laboratory of Horticultural Crop Biology and Germplasm Creation in Southwest China, Ministry of Agriculture and Rural Affairs, Chengdu 610066, China
| | - Meiyan Tu
- Institute of Horticulture, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (C.H.); (L.W.); (Y.L.); (K.Z.); (K.Z.); (D.C.); (J.L.); (H.S.)
- Key Laboratory of Horticultural Crop Biology and Germplasm Creation in Southwest China, Ministry of Agriculture and Rural Affairs, Chengdu 610066, China
| |
Collapse
|
|
2
|
He Q, Chen B, Zheng H, Cao Y, Hua M, Yin Y, Peng J, Li J, Chen J, Yan F, Song X, Lin L. Complete genome sequence of Paris polyphylla chlorotic mottle virus infecting Paris polyphylla var. yunnanensis in southwest China. Arch Virol 2023; 168:292. [PMID: 37966521 DOI: 10.1007/s00705-023-05896-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 08/25/2023] [Indexed: 11/16/2023]
Abstract
A novel virus infecting a Paris polyphylla var. yunnanensis plant, tentatively named "Paris polyphylla chlorotic mottle virus" (PpCMV), was discovered in the city of Lijiang, Yunnan Province, China. Its genome consists of 6384 nucleotides (nt), excluding the 3'-terminal poly(A) tail, and contains two open reading frames: ORF1 and ORF2. ORF1 is 6150 nt in length, encoding a large 2050-aa polyprotein with at least two conserved regions encoding a replication-associated protein and a coat protein, the latter of which is located at the 3' end of ORF1. ORF2, consisting of 1185 nt, is located within ORF1 but has a different reading frame. It encodes a 394-aa-long putative movement protein. Phylogenetic analysis based on amino acid sequences revealed that the newly discovered virus exhibited the closest relationship to Hobart betaflexivirus 1 and rhodiola betaflexivirus 1, both of which belong to the genus Capillovirus, sharing 48.8% and 36.5% amino acid sequence identity, respectively, in the structural protein. This is the first report of the complete genome sequence of PpCMV in China.
Collapse
Affiliation(s)
- Qiongji He
- Institute of Alpine Economics and Botany, Yunnan Academy of Agricultural Sciences, Yunnan, China
| | - Binghua Chen
- Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang, 550025, China
- 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 MOA of China and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Hongying Zheng
- 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 MOA of China and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Yuhao Cao
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo, 315211, China
| | - Mengyin Hua
- 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 MOA of China and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Yueyan Yin
- 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 MOA of China and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Jiejun Peng
- 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 MOA of China and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Junmin 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 MOA of China and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Jianping 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 MOA of China and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Fei Yan
- 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 MOA of China and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China.
| | - Xuemei Song
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo, 315211, China.
| | - Lin Lin
- 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 MOA of China and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China.
| |
Collapse
|
|
3
|
Silva JMF, Melo FL, Elena SF, Candresse T, Sabanadzovic S, Tzanetakis IE, Blouin AG, Villamor DEV, Mollov D, Constable F, Cao M, Saldarelli P, Cho WK, Nagata T. Virus classification based on in-depth sequence analyses and development of demarcation criteria using the Betaflexiviridae as a case study. J Gen Virol 2022; 103. [DOI: 10.1099/jgv.0.001806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Currently, many viruses are classified based on their genome organization and nucleotide/amino acid sequence identities of their capsid and replication-associated proteins. Although biological traits such as vector specificities and host range are also considered, this later information is scarce for the majority of recently identified viruses, characterized only from genomic sequences. Accordingly, genomic sequences and derived information are being frequently used as the major, if not only, criteria for virus classification and this calls for a full review of the process. Herein, we critically addressed current issues concerning classification of viruses in the family Betaflexiviridae in the era of high-throughput sequencing and propose an updated set of demarcation criteria based on a process involving pairwise identity analyses and phylogenetics. The proposed framework has been designed to solve the majority of current conundrums in taxonomy and to facilitate future virus classification. Finally, the analyses performed herein, alongside the proposed approaches, could be used as a blueprint for virus classification at-large.
Collapse
Affiliation(s)
- João Marcos Fagundes Silva
- Departamento de Biologia Celular, Instituto de Ciências Biológicas, University of Brasília, Brasília 70910-900, Brazil
| | - Fernando Lucas Melo
- Departamento de Fitopatologia, Instituto de Biología Integrativa de Sistemas, University of Brasília, Brasília 70910-900, Brazil
| | - Santiago F. Elena
- The Santa Fe Institute, Santa Fe, NM 87501, USA
- Instituto de Biología Integrativa de Sistemas (I2 13 SysBio), CSIC-Universitat de València, Paterna 14 46980 València, Spain
| | - Thierry Candresse
- Univ. Bordeaux, INRAE, UMR 1332 BFP, 33140 Villenave d’Ornon, France
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA
| | | | - Arnaud G. Blouin
- Virology-Phytoplasmology Laboratory, Agroscope, 1260 Nyon, Switzerland
| | | | - Dimitre Mollov
- USDA-ARS Horticultural Crops Disease and Pest Management Research Unit, Corvallis, OR, 97330, USA
| | - Fiona Constable
- Department of Jobs Precincts and Regions, Agriculture Victoria Research, Agribio, Bundoora, VIC 3083, Australia
| | - Mengji Cao
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing 400712, PR China
| | - Pasquale Saldarelli
- National Research Council of Italy (CNR), Institute for Sustainable Plant Protection (IPSP), Via Amendola 122/D, 70126 Bari, Italy
| | - Won Kyong Cho
- College of Biotechnology and Bioengineering, Sungkyunkwan University, Seoburo 2066, Suwon 16419, Gyeonggi, Republic of Korea
| | - Tatsuya Nagata
- Departamento de Biologia Celular, Instituto de Ciências Biológicas, University of Brasília, Brasília 70910-900, Brazil
| |
Collapse
|
|
4
|
Ma Y, Che H, Gao S, Lin Y, Li S. Diverse Novel Viruses Coinfecting the Tropical Ornamental Plant Polyscias balfouriana in China. Viruses 2022; 14:v14061120. [PMID: 35746592 PMCID: PMC9228080 DOI: 10.3390/v14061120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 05/20/2022] [Accepted: 05/21/2022] [Indexed: 12/10/2022] Open
Abstract
The viromic profile of Polyscias balfouriana cv. Marginata, a perennial woody and ornamental plant, was determined using ribosomal RNA-depleted total RNA (rRNA-depleted totRNA) sequencing. Five viruses (i.e., polyscias mosaic virus, PoMV; one potential novel rhabdovirus; and three novel viruses of Betaflexiviridae and Closteroviridae) were detected and prevalence-surveyed in Hainan province, China. The genomes of polyscias capillovirus 1 (PCaV-1) and polyscias citrivirus 1 (PCiV-1) of family Betaflexiviridae were completed, and the genomes of polyscias crinivirus 1 (PCrV-1) of Closteroviridae were nearly completed lacking the 5′ and 3′ termini. PCaV-1 shares 68% genome nucleotide (nt) identity and 66% replicase (Rep) amino acid (aa) identity with homologues in apple stem grooving virus (ASGV). PCiV-1 shares 65% genome nt identity and 64% Rep aa identity with homologs in citrus leaf blotch virus (CLBV). Meeting the species demarcation criteria, PCaV-1 and PCiV-1 were considered to be new species in genera Capillovirus and Citrivirus, respectively. PCrV-1 shares high genome nt identity (62%), heat shock protein 70-like protein (HSP70h) and RNA-dependent RNA polymerase (RdRp) aa identity (78−80%) with homologues in tomato chlorosis virus (ToCV). We tentatively consider PCrV-1 to be an unclassified member of the Crinivirus genus. PoMV, PCaV-1, PCiV-1, and PCrV-1 are the prevalent viruses with >73% occurrence in the Xinglong Tropical Botanical Garden, Hainan, China.
Collapse
Affiliation(s)
- Yuxin Ma
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (Y.M.); (H.C.); (Y.L.)
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering/Key Laboratory of Ministry of Education, Guizhou University, Guiyang 550025, China
| | - Haiyan Che
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (Y.M.); (H.C.); (Y.L.)
| | - Shengfeng Gao
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning 571533, China;
| | - Yating Lin
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (Y.M.); (H.C.); (Y.L.)
| | - Shifang Li
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (Y.M.); (H.C.); (Y.L.)
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Correspondence:
| |
Collapse
|
|
5
|
Canales C, Morán F, Olmos A, Ruiz-García AB. First Detection and Molecular Characterization of Apple Stem Grooving Virus, Apple Chlorotic Leaf Spot Virus, and Apple Hammerhead Viroid in Loquat in Spain. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112293. [PMID: 34834655 PMCID: PMC8624106 DOI: 10.3390/plants10112293] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/20/2021] [Accepted: 10/21/2021] [Indexed: 06/12/2023]
Abstract
Loquat (Eriobotrya japonica) is an important crop in Spain. To date, only one viral species, apple stem pitting virus (ASPV), has been detected in Spanish loquat orchards. In this study, the presence of additional viruses infecting this crop in Spain was investigated. RT-PCR and high-throughput sequencing (HTS) of symptomatic loquat plants led to first-time detection and characterization of apple stem grooving virus (ASGV), also known as citrus tatter leaf virus (CTLV), and apple chlorotic leaf spot virus (ACLSV) from Spain with description of nearly complete genomic sequences. The frequency of ACLSV infection was the highest, with over 30% of the samples testing positive and were also detected as coinfections with ASGV and ASPV, although most of the samples infected were symptomless. Studies on all the full-length sequences available in the databases were performed in order to establish the phylogenetic relationships of the Spanish isolates of these two viral species. Moreover, apple hammerhead viroid (AHVd) was also detected to infect loquat, the first host different from apple reported for this viroid to date.
Collapse
|
|
6
|
Morán F, Canales C, Olmos A, Ruiz-García AB. Loquat ( Eriobotrya japonica) is a New Natural Host of Apple Stem Pitting Virus. PLANTS 2020; 9:plants9111560. [PMID: 33202713 PMCID: PMC7696262 DOI: 10.3390/plants9111560] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/05/2020] [Accepted: 11/11/2020] [Indexed: 01/09/2023]
Abstract
Loquat (Eriobotrya japonica) is a minor but important woody crop cultivated in Asia and Europe. High-throughput sequencing (HTS) analysis of an asymptomatic loquat plant using RNAseq Illumina technology has allowed the detection for the first time of apple stem pitting virus (ASPV), the type species of the genus Foveavirus in the family Betaflexiviridae, infecting this crop. A nearly complete genome of 9303 nts (ASPV-SL61) reconstructed bioinformatically shows the typical genomic structure of this viral species and a highest nucleotide identity (85.9%) with the Chinese ASPV isolate YLX from pear. A close phylogenetic relationship between ASPV-SL61 and ASPV-YLX has been confirmed by the sequence analysis of full-length ASPV genomic sequences available in the databases. In fact, a phylogenetic study based on a partial CP N-terminal sequence previously proposed to be involved in host adaptation has shown that ASPV-SL61 loquat isolate is more closely related to ASPV pear isolates. The presence of ASPV in loquat has been further confirmed by RT-PCR and Sanger sequencing and DAS-ELISA. An incidence of 15% was determined in one of the loquat Spanish growing areas. The sequence analysis of the partial CP sequences amplified by RT-PCR has shown a high level of variability between loquat isolates. To our knowledge, this is the first record of loquat as a natural host of ASPV.
Collapse
|