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Alfaro-Fernández A, Taengua R, Font-San-Ambrosio I, Sanahuja-Edo E, Peiró R, Galipienso L, Rubio L. Genetic Variation and Evolutionary Analysis of Eggplant Mottled Dwarf Virus Isolates from Spain. PLANTS (BASEL, SWITZERLAND) 2024; 13:250. [PMID: 38256804 PMCID: PMC10818716 DOI: 10.3390/plants13020250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/09/2024] [Accepted: 01/11/2024] [Indexed: 01/24/2024]
Abstract
The genetic variation and population structure of gene N (nucleocapsid) and part of gene L (replicase) from 13 eggplant mottle dwarf virus (EMDV) isolates from Spain were evaluated and compared with sequences of EMDV isolates from other countries retrieved from GenBank. Phylogenetic inference of part of gene L showed three main clades, one containing an EMDV isolate from Australia and the other two containing isolates from Iran and Europe, as well as four subclades. EMDV isolates from Spain were genetically very similar and grouped in a subclade together with one isolate from Germany and one from the UK. No new recombination events were detected in addition to one recombination previously reported, suggesting that recombination is rare for EMDV. The comparison of synonymous and non-synonymous rates showed that negative selection played an important role, and only two codons were under positive selection. Genetic differentiation (Fst test), phylogenetic and nucleotide diversity analyses suggest a unique introduction of EMDV to Spain and low gene flow with other countries. In contrast, Greece and Italy showed diverse populations with high gene flow between both.
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Affiliation(s)
- Ana Alfaro-Fernández
- Instituto Agroforestal Mediterráneo (IAM), Universitat Politècnica de València (UPV), 46022 Valencia, Valencia, Spain; (A.A.-F.); (I.F.-S.-A.); (E.S.-E.)
| | - Rafael Taengua
- Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Moncada, Valencia, Spain; (R.T.); (L.G.)
| | - Isabel Font-San-Ambrosio
- Instituto Agroforestal Mediterráneo (IAM), Universitat Politècnica de València (UPV), 46022 Valencia, Valencia, Spain; (A.A.-F.); (I.F.-S.-A.); (E.S.-E.)
| | - Esmeralda Sanahuja-Edo
- Instituto Agroforestal Mediterráneo (IAM), Universitat Politècnica de València (UPV), 46022 Valencia, Valencia, Spain; (A.A.-F.); (I.F.-S.-A.); (E.S.-E.)
| | - Rosa Peiró
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universitat Politècnica de València (UPV), 46022 Valencia, Valencia, Spain;
| | - Luis Galipienso
- Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Moncada, Valencia, Spain; (R.T.); (L.G.)
| | - Luis Rubio
- Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Moncada, Valencia, Spain; (R.T.); (L.G.)
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Knierim D, Menzel W, Winter S. Immunocapture of virions with virus-specific antibodies prior to high-throughput sequencing effectively enriches for virus-specific sequences. PLoS One 2019; 14:e0216713. [PMID: 31071169 PMCID: PMC6542260 DOI: 10.1371/journal.pone.0216713] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 04/26/2019] [Indexed: 12/21/2022] Open
Abstract
Virus discovery based on high-throughput sequencing relies on enrichment for virus sequences prior to library preparation to achieve a sufficient number of viral reads. In general, preparations of double-stranded RNA or total RNA preparations treated to remove rRNA are used for sequence enrichment. We used virus-specific antibodies to immunocapture virions from plant sap to conduct cDNA synthesis, followed by library preparation and HTS. For the four potato viruses PLRV, PVY, PVA and PYV, template preparation by virion immunocapture provided a simpler and less expensive method than the enrichment of total RNA by ribosomal depletion. Specific enrichment of viral sequences without an intermediate amplification step was achieved, and this high coverage of sequences across the viral genomes was important to identify rare sequence variations. Using this approach, the first complete genome sequence of a potato yellowing virus isolate (PYV, DSMZ PV-0706) was determined in this study. PYV can be confidently assigned as a distinct species in the genus Ilarvirus.
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Affiliation(s)
- Dennis Knierim
- Leibniz-Institute DSMZ—German Collection of Microorganisms
and Cell Cultures, Plant Virus Department, Braunschweig,
Germany
| | - Wulf Menzel
- Leibniz-Institute DSMZ—German Collection of Microorganisms
and Cell Cultures, Plant Virus Department, Braunschweig,
Germany
- * E-mail:
| | - Stephan Winter
- Leibniz-Institute DSMZ—German Collection of Microorganisms
and Cell Cultures, Plant Virus Department, Braunschweig,
Germany
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Lan Y, Yan Z, Guo Y, Duan T, Li C, Gao P, Christensen MJ. RETRACTED ARTICLE: Albinism and mosaicism in Apocynum venetum associated with viral infections in China. Arch Virol 2019; 164:333. [PMID: 30267156 DOI: 10.1007/s00705-018-4059-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 09/18/2018] [Indexed: 10/28/2022]
Affiliation(s)
- Yanru Lan
- State Key Laboratory of Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, China
- Agriculture Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou, China
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Zhichen Yan
- State Key Laboratory of Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, China
- Agriculture Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou, China
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Yane Guo
- State Key Laboratory of Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, China
- Agriculture Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou, China
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Tingyu Duan
- State Key Laboratory of Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, China.
- Agriculture Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou, China.
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China.
| | - Chunjie Li
- State Key Laboratory of Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, China
- Agriculture Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou, China
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Peng Gao
- State Key Laboratory of Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, China
- Agriculture Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou, China
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Michael J Christensen
- State Key Laboratory of Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, China
- Agriculture Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou, China
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
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Kim H, Park D, Hahn Y. Identification of novel RNA viruses in alfalfa (Medicago sativa): an Alphapartitivirus, a Deltapartitivirus, and a Marafivirus. Gene 2017; 638:7-12. [PMID: 28974471 DOI: 10.1016/j.gene.2017.09.069] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 09/13/2017] [Accepted: 09/29/2017] [Indexed: 12/16/2022]
Abstract
Genomic RNA molecules of plant RNA viruses are often co-isolated with the host RNAs, and their sequences can be detected in plant transcriptome datasets. Here, an alfalfa (Medicago sativa) transcriptome dataset was analyzed and three new RNA viruses were identified, which were named Medicago sativa alphapartitivirus 1 (MsAPV1), Medicago sativa deltapartitivirus 1 (MsDPV1), and Medicago sativa marafivirus 1 (MsMV1). The RNA-dependent RNA polymerases of MsAPV1, MsDPV1, and MsMV1 showed about 68%, 58%, and 46% amino acid sequence identity, respectively, with their closest virus species. Sequence similarity and phylogenetic analyses indicated that MsAPV1, MsDPV1, and MsMV1 were novel RNA virus species that belong to the genus Alphapartitivirus of the family Partitiviridae, the genus Deltapartitivirus of the family Partitiviridae, and the genus Marafivirus of the family Tymoviridae, respectively. The bioinformatics procedure applied in this study may facilitate the identification of novel RNA viruses from plant transcriptome data.
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Affiliation(s)
- Hyein Kim
- Department of Life Science, Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul 06974, South Korea
| | - Dongbin Park
- Department of Life Science, Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul 06974, South Korea
| | - Yoonsoo Hahn
- Department of Life Science, Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul 06974, South Korea.
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