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Pouraziz P, Yousefi M, Santosa AI, Koolivand D. Genetic Variation between Asian and Mediterranean Populations of Cucurbit Aphid-Borne Yellows Virus. Viruses 2023; 15:1714. [PMID: 37632056 PMCID: PMC10457933 DOI: 10.3390/v15081714] [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: 06/26/2023] [Revised: 07/16/2023] [Accepted: 07/17/2023] [Indexed: 08/27/2023] Open
Abstract
Viral symptoms, such as yellowing, leaf deformation, mottling, vein clearing, and reduced yield, were observed in cucurbits in Iran. This study aimed to detect the main suspected causal agent, cucurbit aphid-borne yellows virus (CABYV), in Iran and analyze the genetic diversity among isolates. Two hundred samples were collected from different growing areas between 2019 and 2022. PCR amplification was performed on the P3 and P4 genes. The sequences of 18 Iranian isolates were obtained and deposited in GenBank. Recombination, phylogenetic, and population genetics studies were then carried out for the complete genome and all ORFs sequences, together with other isolates in GenBank. The nucleotide identities of the overlapped ORF3/4 sequences of Iranian isolates were 94.8 to 99.5% among themselves, and with other tested isolates ranging from 94.3 to 99.3%. Phylogenetic trees based on the complete genome and the overlapped ORF3/4 showed two major clades, namely Asian and Mediterranean, and the new isolates from Iran were positioned in both clades. The obtained results also suggest that all the genes and two clades of CABYV populations were under negative selection pressure. Furthermore, rare gene flow between these two clades (FST > 0.33) confirmed the high genetic separation among them.
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Affiliation(s)
- Parastoo Pouraziz
- Department of Plant Protection, Faculty of Agriculture, University of Zanjan, Zanjan 45371-38111, Iran (D.K.)
| | - Milad Yousefi
- Department of Plant Protection, Faculty of Agriculture, University of Zanjan, Zanjan 45371-38111, Iran (D.K.)
| | - Adyatma Irawan Santosa
- Department of Plant Protection, Faculty of Agriculture, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
| | - Davoud Koolivand
- Department of Plant Protection, Faculty of Agriculture, University of Zanjan, Zanjan 45371-38111, Iran (D.K.)
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Vidal AH, Lacorte C, Sanches MM, Alves-Freitas DMT, Abreu EFM, Pinheiro-Lima B, Rosa RCC, Jesus ON, Campos MA, Felix GP, Abreu ACR, Santos YS, Lacerda ALM, Varsani A, Melo FL, Ribeiro SG. Characterization of Cucurbit Aphid-Borne Yellows Virus (CABYV) from Passion Fruit in Brazil: Evidence of a Complex of Species within CABYV Isolates. Viruses 2023; 15:v15020410. [PMID: 36851624 PMCID: PMC9965994 DOI: 10.3390/v15020410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/25/2023] [Accepted: 01/28/2023] [Indexed: 02/05/2023] Open
Abstract
High-throughput sequencing (HTS) has been an important tool for the discovery of plant viruses and their surveillance. In 2015, several virus-like symptoms were observed in passion fruit (PF) plants in Bahia state, Brazil. Using HTS technology, bioinformatics tools, RT-PCR, and Sanger sequencing, we identified the cucurbit aphid-borne yellows virus (CABYV, Polerovirus, Solemoviridae) in co-infection with cowpea aphid-borne mosaic virus (CABMV, Potyvirus, Potyviridae) in PF, in green manure, and spontaneous plants in several localities in Bahia. Complete genomes of CABYV-PF isolates were determined and analyzed with other CABYV isolates available in GenBank that have been identified in various countries. Phylogenetic analysis and pairwise identity comparison with CABYV isolates showed that CABYV-PFs are more closely related to French and Spanish isolates. Overall, analyses of all the CABYV genomes revealed that these could represent ten distinct species, and we thus proposed reclassifying these CABYV as isolates into ten species, tentatively named "Polerovirus curcubitaeprimum" to "Polerovirus curcubitaenonum", and "Polerovirus melo". CABYV-PF is a member of "Polerovirus curcubitaeprimum".
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Affiliation(s)
- Andreza H. Vidal
- Embrapa Recursos Genéticos e Biotecnologia, Brasília 70770-917, DF, Brazil
- Instituto de Ciências Biológicas—IB, PPG BIOMOL, Universidade de Brasília, Brasília 70910-900, DF, Brazil
| | - Cristiano Lacorte
- Embrapa Recursos Genéticos e Biotecnologia, Brasília 70770-917, DF, Brazil
| | - Marcio M. Sanches
- Embrapa Recursos Genéticos e Biotecnologia, Brasília 70770-917, DF, Brazil
- Embrapa Gado de Corte, Campo Grande 79106-550, MS, Brazil
| | | | | | - Bruna Pinheiro-Lima
- Embrapa Recursos Genéticos e Biotecnologia, Brasília 70770-917, DF, Brazil
- Instituto de Ciências Biológicas—IB, PPG BIOMOL, Universidade de Brasília, Brasília 70910-900, DF, Brazil
| | | | - Onildo N. Jesus
- Embrapa Mandioca e Fruticultura, Cruz das Almas 44380-000, BA, Brazil
| | - Magnólia A. Campos
- Centro de Educação e Saúde, Universidade Federal de Campina Grande, Cuité 58175-000, PB, Brazil
| | - Gustavo P. Felix
- Embrapa Recursos Genéticos e Biotecnologia, Brasília 70770-917, DF, Brazil
- Instituto de Ciências Biológicas—IB, Universidade de Brasília, Brasília 70910-900, DF, Brazil
| | - Ana Clara R. Abreu
- Embrapa Recursos Genéticos e Biotecnologia, Brasília 70770-917, DF, Brazil
- Instituto de Ciências Biológicas—IB, Universidade de Brasília, Brasília 70910-900, DF, Brazil
| | - Yam S. Santos
- Embrapa Recursos Genéticos e Biotecnologia, Brasília 70770-917, DF, Brazil
- Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa (UFV), Viçosa 36570-900, MG, Brazil
| | | | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Fernando L. Melo
- Instituto de Ciências Biológicas—IB, PPG BIOMOL, Universidade de Brasília, Brasília 70910-900, DF, Brazil
| | - Simone G. Ribeiro
- Embrapa Recursos Genéticos e Biotecnologia, Brasília 70770-917, DF, Brazil
- Instituto de Ciências Biológicas—IB, PPG BIOMOL, Universidade de Brasília, Brasília 70910-900, DF, Brazil
- Correspondence:
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Khanal V, Ali A. High Mutation Frequency and Significant Population Differentiation in Papaya Ringspot Virus-W Isolates. Pathogens 2021; 10:pathogens10101278. [PMID: 34684227 PMCID: PMC8537659 DOI: 10.3390/pathogens10101278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/29/2021] [Accepted: 09/30/2021] [Indexed: 11/18/2022] Open
Abstract
A total of 101 papaya ringspot virus-W (PRSV-W) isolates were collected from five different cucurbit hosts in six counties of Oklahoma during the 2016–2018 growing seasons. The coat protein (CP) coding region of these isolates was amplified by reverse transcription-polymerase chain reaction, and 370 clones (3–5 clones/isolate) were sequenced. Phylogenetic analysis revealed three phylogroups while host, location, and collection time of isolates had minimal impact on grouping pattern. When CP gene sequences of these isolates were compared with sequences of published PRSV isolates (both P and W strains), they clustered into four phylogroups based on geographical location. Oklahoman PRSV-W isolates formed one of the four distinct major phylogroups. The permutation-based tests, including Ks, Ks *, Z *, Snn, and neutrality tests, indicated significant genetic differentiation and polymorphisms among PRSV-W populations in Oklahoma. The selection analysis confirmed that the CP gene is undergoing purifying selection. The mutation frequencies among all PRSV-W isolates were within the range of 1 × 10−3. The substitution mutations in 370 clones of PRSV-W isolates showed a high proportion of transition mutations, which gave rise to higher GC content. The N-terminal region of the CP gene mostly contained the variable sites with numerous mutational hotspots, while the core region was highly conserved.
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High Prevalence of Three Potyviruses Infecting Cucurbits in Oklahoma and Phylogenetic Analysis of Cucurbit Aphid-Borne Yellows Virus Isolated from Pumpkins. Pathogens 2021; 10:pathogens10010053. [PMID: 33430063 PMCID: PMC7828045 DOI: 10.3390/pathogens10010053] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 12/31/2020] [Accepted: 01/03/2021] [Indexed: 01/23/2023] Open
Abstract
Field information about viruses infecting crops is fundamental for understanding the severity of the effects they cause in plants. To determine the status of cucurbit viruses, surveys were conducted for three consecutive years (2016–2018) in different agricultural districts of Oklahoma. A total of 1331 leaf samples from >90 fields were randomly collected from both symptomatic and asymptomatic cucurbit plants across 11 counties. All samples were tested with the dot-immunobinding assay (DIBA) against the antisera of 10 known viruses. Samples infected with papaya ringspot virus (PRSV-W), watermelon mosaic virus (WMV), zucchini yellow mosaic virus (ZYMV), and cucurbit aphid-borne-yellows virus (CABYV) were also tested by RT-PCR. Of the 10 viruses, PRSV-W was the most widespread, with an overall prevalence of 59.1%, present in all 11 counties, followed by ZYMV (27.6%), in 10 counties, and WMV (20.7%), in seven counties, while the remaining viruses were present sporadically with low incidence. Approximately 42% of the infected samples were positive, with more than one virus indicating a high proportion of mixed infections. CABYV was detected for the first time in Oklahoma, and the phylogenetic analysis of the first complete genome sequence of a CABYV isolate (BL-4) from the US showed a close relationship with Asian isolates.
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