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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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Miras M, Aranda MA, Truniger V. Different RNA Elements Control Viral Protein Synthesis in Polerovirus Isolates Evolved in Separate Geographical Regions. Int J Mol Sci 2022; 23:ijms232012503. [PMID: 36293360 PMCID: PMC9603980 DOI: 10.3390/ijms232012503] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/13/2022] [Accepted: 10/15/2022] [Indexed: 12/05/2022] Open
Abstract
Most plant viruses lack the 5′-cap and 3′-poly(A) structures, which are common in their host mRNAs, and are crucial for translation initiation. Thus, alternative translation initiation mechanisms were identified for viral mRNAs, one of these being controlled by an RNA element in their 3′-ends that is able to enhance mRNA cap-independent translation (3′-CITE). The 3′-CITEs are modular and transferable RNA elements. In the case of poleroviruses, the mechanism of translation initiation of their RNAs in the host cell is still unclear; thus, it was studied for one of its members, cucurbit aphid-borne yellows virus (CABYV). We determined that efficient CABYV RNA translation requires the presence of a 3′-CITE in its 3′-UTR. We showed that this 3′-CITE requires the presence of the 5′-UTR in cis for its eIF4E-independent activity. Efficient virus multiplication depended on 3′-CITE activity. In CABYV isolates belonging to the three phylogenetic groups identified so far, the 3′-CITEs differ, and recombination prediction analyses suggest that these 3′-CITEs have been acquired through recombination with an unknown donor. Since these isolates have evolved in different geographical regions, this may suggest that their respective 3′-CITEs are possibly better adapted to each region. We propose that translation of other polerovirus genomes may also be 3′-CITE-dependent.
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Affiliation(s)
- Manuel Miras
- Centro de Edafología y Biología Aplicada del Segura, Consejo Superior de Investigaciones Científicas (CEBAS-CSIC), 30100 Murcia, Spain
- Department of Molecular Physiology, Heinrich Heine University of Düsseldorf, 40225 Düsseldorf, Germany
| | - Miguel A. Aranda
- Centro de Edafología y Biología Aplicada del Segura, Consejo Superior de Investigaciones Científicas (CEBAS-CSIC), 30100 Murcia, Spain
| | - Verónica Truniger
- Centro de Edafología y Biología Aplicada del Segura, Consejo Superior de Investigaciones Científicas (CEBAS-CSIC), 30100 Murcia, Spain
- Correspondence:
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Maina S, Barbetti MJ, Edwards OR, Minemba D, Areke MW, Jones RAC. Zucchini yellow mosaic virus Genomic Sequences from Papua New Guinea: Lack of Genetic Connectivity with Northern Australian or East Timorese Genomes, and New Recombination Findings. PLANT DISEASE 2019; 103:1326-1336. [PMID: 30995424 DOI: 10.1094/pdis-09-18-1666-re] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Zucchini yellow mosaic virus (ZYMV) isolates were obtained in Papua New Guinea (PNG) from cucumber (Cucumis sativus) or pumpkin (Cucurbita spp.) plants showing mosaic symptoms growing at Kongop in the Mount Hagen District, Western Highlands Province, or Zage in the Goroka District, Eastern Highlands Province. The samples were blotted onto FTA cards, which were sent to Australia, where they were subjected to high-throughput sequencing. When the coding regions of the nine new ZYMV genomic sequences found were compared with those of 64 other ZYMV sequences from elsewhere, they grouped together, forming new minor phylogroup VII within ZYMV's major phylogroup A. Genetic connectivity was lacking between ZYMV genomic sequences from PNG and its neighboring countries, Australia and East Timor; the closest match between a PNG and any other genomic sequence was a 92.8% nucleotide identity with a sequence in major phylogroup A's minor phylogroup VI from Japan. When the RDP5.2 recombination analysis program was used to compare 66 ZYMV sequences, evidence was obtained of 30 firm recombination events involving 41 sequences, and all isolates from PNG were recombinants. There were 21 sequences without recombination events in major phylogroup A, whereas there were only 4 such sequences within major phylogroup B. ZYMV's P1, Cl, N1a-Pro, P3, CP, and NIb regions contained the highest evidence of recombination breakpoints. Following removal of recombinant sequences, seven minor phylogroups were absent (I, III, IV, V, VI, VII, and VIII), leaving only minor phylogroups II and IX. By contrast, when a phylogenetic tree was constructed using recombinant sequences with their recombinationally derived tracts removed before analysis, five previous minor phylogroups remained unchanged within major phylogroup A (II, III, IV, V, and VII) while four formed two new merged phylogroups (I/VI and VIII/IX). Absence of genetic connectivity between PNG, Australian, and East Timorese ZYMV sequences, and the 92.8% nucleotide identity between a PNG sequence and the closest sequence from elsewhere, suggest that a single introduction may have occurred followed by subsequent evolution to adapt to the PNG environment. The need for enhanced biosecurity measures to protect against potentially damaging virus movements crossing the seas separating neighboring countries in this region of the world is discussed.
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Affiliation(s)
- Solomon Maina
- 1 School of Agriculture and Environment, Faculty of Science, and
- 2 UWA Institute of Agriculture, Faculty of Science, The University of Western Australia, Crawley, WA, Australia
- 3 Cooperative Research Centre for Plant Biosecurity, Canberra, Australian Capital Territory, Australia
| | - Martin J Barbetti
- 1 School of Agriculture and Environment, Faculty of Science, and
- 2 UWA Institute of Agriculture, Faculty of Science, The University of Western Australia, Crawley, WA, Australia
- 3 Cooperative Research Centre for Plant Biosecurity, Canberra, Australian Capital Territory, Australia
| | - Owain R Edwards
- 3 Cooperative Research Centre for Plant Biosecurity, Canberra, Australian Capital Territory, Australia
- 4 Commonwealth Scientific and Industrial Research Organisation Land and Water, Floreat Park, WA 6014, Australia
| | - David Minemba
- 1 School of Agriculture and Environment, Faculty of Science, and
- 5 The National Agricultural Research Institute, PO Box 4415, Lae, Morobe Province, Papua New Guinea
| | - Michael W Areke
- 6 National Agriculture Quarantine and Inspection Authority, PO Box 741, Port Moresby, National Capital District, Papua New Guinea; and
| | - Roger A C Jones
- 2 UWA Institute of Agriculture, Faculty of Science, The University of Western Australia, Crawley, WA, Australia
- 3 Cooperative Research Centre for Plant Biosecurity, Canberra, Australian Capital Territory, Australia
- 7 Department of Primary Industries and Regional Development, South Perth, WA, Australia
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Maina S, Barbetti MJ, Edwards OR, Minemba D, Areke MW, Jones RAC. Genetic Connectivity Between Papaya Ringspot Virus Genomes from Papua New Guinea and Northern Australia, and New Recombination Insights. PLANT DISEASE 2019; 103:737-747. [PMID: 30856073 DOI: 10.1094/pdis-07-18-1136-re] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Isolates of papaya ringspot virus (PRSV) were obtained from plants of pumpkin (Cucurbita spp.) or cucumber (Cucumis sativus) showing mosaic symptoms growing at Zage in Goroka District in the Eastern Highland Province of Papua New Guinea (PNG) or Bagl in the Mount Hagen District, Western Highlands Province. The samples were sent to Australia on FTA cards where they were subjected to High Throughput Sequencing (HTS). When the coding regions of the six new PRSV genomic sequences obtained via HTS were compared with those of 54 other complete PRSV sequences from other parts of the world, all six grouped together with the 12 northern Australian sequences within major phylogroup B minor phylogroup I, the Australian sequences coming from three widely dispersed locations spanning the north of the continent. Notably, none of the PNG isolates grouped with genomic sequences from the nearby country of East Timor in phylogroup A. The closest genetic match between Australian and PNG sequences was a nucleotide (nt) sequence identity of 96.9%, whereas between PNG and East Timorese isolates it was only 83.1%. These phylogenetic and nt identity findings demonstrate genetic connectivity between PRSV populations from PNG and Australia. Recombination analysis of the 60 PRSV sequences available revealed evidence of 26 recombination events within 18 isolates, only four of which were within major phylogroup B and none of which were from PNG or Australia. Within the recombinant genomes, the P1, Cl, NIa-Pro, NIb, 6K2, and 5'UTR regions contained the highest numbers of recombination breakpoints. After removal of nonrecombinant sequences, four minor phylogroups were lost (IV, VII, VIII, XV), only one of which was in phylogroup B. When genome regions from which recombinationally derived tracts of sequence were removed from recombinants prior to alignment with nonrecombinant genomes, seven previous minor phylogroups within major phylogroup A, and two within major phylogroup B, merged either partially or entirely forming four merged minor phylogroups. The genetic connectivity between PNG and northern Australian isolates and absence of detectable recombination within either group suggests that PRSV isolates from East Timor, rather than PNG, might pose a biosecurity threat to northern Australian agriculture should they prove more virulent than those already present.
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Affiliation(s)
- Solomon Maina
- 1 School of Agriculture and Environment, Faculty of Science, The University of Western Australia, Crawley, WA, Australia
- 2 UWA Institute of Agriculture, Faculty of Science, The University of Western Australia, Crawley, WA, Australia
- 3 Cooperative Research Centre for Plant Biosecurity, Canberra, ACT, Australia
| | - Martin J Barbetti
- 1 School of Agriculture and Environment, Faculty of Science, The University of Western Australia, Crawley, WA, Australia
- 2 UWA Institute of Agriculture, Faculty of Science, The University of Western Australia, Crawley, WA, Australia
- 3 Cooperative Research Centre for Plant Biosecurity, Canberra, ACT, Australia
| | - Owain R Edwards
- 3 Cooperative Research Centre for Plant Biosecurity, Canberra, ACT, Australia
- 4 CSIRO Land and Water, Floreat Park, WA6014, Australia
| | - David Minemba
- 1 School of Agriculture and Environment, Faculty of Science, The University of Western Australia, Crawley, WA, Australia
- 5 The National Agriculture Research Institute, P.O. Box 4415, Lae, Morobe Province, Papua New Guinea
| | - Michael W Areke
- 6 National Agriculture Quarantine and Inspection Authority, P.O. Box 741, Port Moresby, National Capital District, Papua New Guinea; and
| | - Roger A C Jones
- 2 UWA Institute of Agriculture, Faculty of Science, The University of Western Australia, Crawley, WA, Australia
- 3 Cooperative Research Centre for Plant Biosecurity, Canberra, ACT, Australia
- 7 Department of Primary Industries and Rural Development Food Western Australia, South Perth, WA, Australia
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Maina S, Barbetti MJ, Martin DP, Edwards OR, Jones RAC. New Isolates of Sweet potato feathery mottle virus and Sweet potato virus C: Biological and Molecular Properties, and Recombination Analysis Based on Complete Genomes. PLANT DISEASE 2018; 102:1899-1914. [PMID: 30136885 DOI: 10.1094/pdis-12-17-1972-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Sweet potato feathery mottle virus (SPFMV) and Sweet potato virus C (SPVC) isolates were obtained from sweetpotato shoot or tuberous root samples from three widely separated locations in Australia's tropical north (Cairns, Darwin, and Kununurra). The samples were planted in the glasshouse and scions obtained from the plants were graft inoculated to Ipomoea setosa plants. Virus symptoms were recorded in the field in Kununurra and in glasshouse-grown sweetpotato and I. setosa plants. RNA extracts from I. setosa leaf samples were subjected to high-throughput sequencing. New complete SPFMV (n = 17) and SPVC (n = 6) genomic sequences were obtained and compared with 47 sequences from GenBank. Phylogenetic analysis revealed that the 17 new SPFMV genomes all fitted within either major phylogroup A, minor phylogroup II, formerly O; or major phylogroup B, formerly RC. Major phylogroup A's minor phylogroup I, formerly EA, only appeared when recombinants were included. Numbers of SPVC genomes were insufficient to subdivide it into phylogroups. Within phylogroup A's minor phylogroup II, the closest genetic match between an Australian and a Southeast Asian SPFMV sequence was the 97.4% nucleotide identity with an East Timorese sequence. Recombination analysis of the 43 SPFMV and 27 SPVC sequences revealed evidence of 44 recombination events, 16 of which involved interspecies sequence transfers between SPFMV and SPVC and 28 intraspecies transfers, 17 in SPFMV and 11 in SPVC. Within SPFMV, 11 intraspecies recombination events were between different major phylogroups and 6 were between members of the same major phylogroup. Phylogenetic analysis accounting for the detected recombination events within SPFMV sequences yielded evidence of minor phylogroup II and phylogroup B but the five sequences from minor phylogroup I were distributed in two separate groups among the sequences of minor phylogroup II. For the SPVC sequences, phylogenetic analysis accounting for the detected recombination events revealed three major phylogroups (A, B, and C), with major phylogroup A being further subdivided into two minor phylogroups. Within the recombinant genomes of both viruses, their PI, NIa-Pro, NIb, and CP genes contained the highest numbers of recombination breakpoints. The high frequency of interspecies and interphylogroup recombination events reflects the widespread occurrence of mixed SPVC and SPFMV infections within sweetpotato plants. The prevalence of infection in northern Australian sweetpotato samples reinforces the need for improved virus testing in healthy sweetpotato stock programs. Furthermore, evidence of genetic connectivity between Australian and East Timorese SPFMV genomes emphasizes the need for improved biosecurity measures to protect against potentially damaging international virus movements.
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Affiliation(s)
- Solomon Maina
- School of Agriculture and Environment and the University of Western Australia (UWA) Institute of Agriculture, Faculty of Science, UWA, Crawley, WA 6009, Australia; and Cooperative Research Centre for Plant Biosecurity, Canberra, ACT 2617, Australia
| | - Martin J Barbetti
- School of Agriculture and Environment and UWA Institute of Agriculture, Faculty of Science, UWA
| | - Darren P Martin
- Institute of Infectious Diseases and Molecular Medicine, Computational Biology Group, University of Cape Town, Cape Town 7549, South Africa
| | - Owain R Edwards
- CSIRO Land and Water, Floreat Park, WA 6014, Australia; and Cooperative Research Centre for Plant Biosecurity, Canberra, ACT 2617, Australia
| | - Roger A C Jones
- Department of Primary Industries and Rural Development, South Perth, WA 6151, Australia; UWA Institute of Agriculture, Faculty of Science, UWA
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