Virome Scanning of Pear Germplasm Collections Identifies a New Velarivirus and Extends the Geographical Spread of Three Other Pear Viruses
In this study, an extensive virome investigation was performed on a germplasm collection of pear trees (Pyrus communis L.) from the Walloon Agricultural Research Centre (Gembloux, Belgium). In total, 128 pear trees samples were analyzed as pools using high-throughput sequencing techniques and/or tes...
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| Language: | English |
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The American Phytopathological Society
2025-03-01
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| Series: | Phytobiomes Journal |
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| Online Access: | https://apsjournals.apsnet.org/doi/10.1094/PBIOMES-03-24-0030-FI |
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| author | Nuria Fontdevila Pareta Carole Gailly Arnaud G. Blouin Beatrix Buchmann Markus Bünter Thierry Candresse Nathalie Dubuis Denis Kutnjak Marc Lateur Anja Pecman Stéphan Steyer Sébastien Massart |
| author_facet | Nuria Fontdevila Pareta Carole Gailly Arnaud G. Blouin Beatrix Buchmann Markus Bünter Thierry Candresse Nathalie Dubuis Denis Kutnjak Marc Lateur Anja Pecman Stéphan Steyer Sébastien Massart |
| author_sort | Nuria Fontdevila Pareta |
| collection | DOAJ |
| description | In this study, an extensive virome investigation was performed on a germplasm collection of pear trees (Pyrus communis L.) from the Walloon Agricultural Research Centre (Gembloux, Belgium). In total, 128 pear trees samples were analyzed as pools using high-throughput sequencing techniques and/or tested individually for targeted viruses by reverse transcription PCR (RT-PCR). During the virome survey, a novel velarivirus was identified in several asymptomatic trees, and four known viruses were detected. Bioinformatics tools were used to assemble the genome of the new virus. The pear germplasm collection from Kozjanski Park (Slovenia) and a viral collection from Agroscope (Nyon, Switzerland) were also surveyed for the new pear virus and for three known viruses (citrus virus A [CiVA], apple rubbery wood virus 1 [ARWV-1], and apple rubbery wood virus 2 [ARWV-2]) to study their prevalence and geographic distribution. In Belgium, the new velarivirus was detected by RT-PCR in 6 of the 99 sampled trees (6%) and CiVA in 49 (49%) of them; in Slovenia, four of the six trees sampled (67%) were positive for CiVA; and in Switzerland, four of the nine trees sampled (44%) were positive for CiVA and 1 (11%) for ARWV-1 and -2. This study combined pooled high-throughput sequencing analyses to maximize the amount of germplasm tested and targeted RT-PCR tests on individual samples for accurate detection. It reports and describes a new velarivirus discovered in pear trees and first detections of CiVA in Belgium, Switzerland, and Slovenia, as well as ARWV-1 and -2 in Switzerland. [Figure: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license. |
| format | Article |
| id | doaj-art-e49c017dd9df4d2b8506b7938d522768 |
| institution | Kabale University |
| issn | 2471-2906 |
| language | English |
| publishDate | 2025-03-01 |
| publisher | The American Phytopathological Society |
| record_format | Article |
| series | Phytobiomes Journal |
| spelling | doaj-art-e49c017dd9df4d2b8506b7938d5227682025-08-20T03:42:14ZengThe American Phytopathological SocietyPhytobiomes Journal2471-29062025-03-0191687910.1094/PBIOMES-03-24-0030-FIVirome Scanning of Pear Germplasm Collections Identifies a New Velarivirus and Extends the Geographical Spread of Three Other Pear VirusesNuria Fontdevila Pareta0Carole Gailly1Arnaud G. Blouin2Beatrix Buchmann3Markus Bünter4Thierry Candresse5Nathalie Dubuis6Denis Kutnjak7Marc Lateur8Anja Pecman9Stéphan Steyer10Sébastien Massart11University of Liège, Gembloux Agro-Bio Tech, Plant Pathology Laboratory, 5030, Gembloux, BelgiumUniversity of Liège, Gembloux Agro-Bio Tech, Plant Pathology Laboratory, 5030, Gembloux, BelgiumAgroscope, Plant Protection Department, 1260, Nyon, SwitzerlandAgroscope, Plant Health Service, 8820, Wädenswil, SwitzerlandAgroscope, Plant Health Service, 8820, Wädenswil, SwitzerlandUniversité de Bordeaux, INRAE, UMR 1332 BFP, 33882, Villenave d'Ornon cedex, FranceAgroscope, Plant Protection Department, 1260, Nyon, SwitzerlandNational Institute of Biology, Department of Biotechnology and Systems Biology, 1000, Ljubljana, SloveniaCentre Wallon de Recherches Agronomiques (CRA-W), Plant and Forest Biodiversity and Breeding, 5030, Gembloux, BelgiumNational Institute of Biology, Department of Biotechnology and Systems Biology, 1000, Ljubljana, SloveniaCentre Wallon de Recherches Agronomiques (CRA-W), Crops and Forest Health, 5030, Gembloux, BelgiumUniversity of Liège, Gembloux Agro-Bio Tech, Plant Pathology Laboratory, 5030, Gembloux, BelgiumIn this study, an extensive virome investigation was performed on a germplasm collection of pear trees (Pyrus communis L.) from the Walloon Agricultural Research Centre (Gembloux, Belgium). In total, 128 pear trees samples were analyzed as pools using high-throughput sequencing techniques and/or tested individually for targeted viruses by reverse transcription PCR (RT-PCR). During the virome survey, a novel velarivirus was identified in several asymptomatic trees, and four known viruses were detected. Bioinformatics tools were used to assemble the genome of the new virus. The pear germplasm collection from Kozjanski Park (Slovenia) and a viral collection from Agroscope (Nyon, Switzerland) were also surveyed for the new pear virus and for three known viruses (citrus virus A [CiVA], apple rubbery wood virus 1 [ARWV-1], and apple rubbery wood virus 2 [ARWV-2]) to study their prevalence and geographic distribution. In Belgium, the new velarivirus was detected by RT-PCR in 6 of the 99 sampled trees (6%) and CiVA in 49 (49%) of them; in Slovenia, four of the six trees sampled (67%) were positive for CiVA; and in Switzerland, four of the nine trees sampled (44%) were positive for CiVA and 1 (11%) for ARWV-1 and -2. This study combined pooled high-throughput sequencing analyses to maximize the amount of germplasm tested and targeted RT-PCR tests on individual samples for accurate detection. It reports and describes a new velarivirus discovered in pear trees and first detections of CiVA in Belgium, Switzerland, and Slovenia, as well as ARWV-1 and -2 in Switzerland. [Figure: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.https://apsjournals.apsnet.org/doi/10.1094/PBIOMES-03-24-0030-FIapple rubbery wood virus 1apple rubbery wood virus 2citrus virus Ahigh-throughput sequencingpearplant virus |
| spellingShingle | Nuria Fontdevila Pareta Carole Gailly Arnaud G. Blouin Beatrix Buchmann Markus Bünter Thierry Candresse Nathalie Dubuis Denis Kutnjak Marc Lateur Anja Pecman Stéphan Steyer Sébastien Massart Virome Scanning of Pear Germplasm Collections Identifies a New Velarivirus and Extends the Geographical Spread of Three Other Pear Viruses Phytobiomes Journal apple rubbery wood virus 1 apple rubbery wood virus 2 citrus virus A high-throughput sequencing pear plant virus |
| title | Virome Scanning of Pear Germplasm Collections Identifies a New Velarivirus and Extends the Geographical Spread of Three Other Pear Viruses |
| title_full | Virome Scanning of Pear Germplasm Collections Identifies a New Velarivirus and Extends the Geographical Spread of Three Other Pear Viruses |
| title_fullStr | Virome Scanning of Pear Germplasm Collections Identifies a New Velarivirus and Extends the Geographical Spread of Three Other Pear Viruses |
| title_full_unstemmed | Virome Scanning of Pear Germplasm Collections Identifies a New Velarivirus and Extends the Geographical Spread of Three Other Pear Viruses |
| title_short | Virome Scanning of Pear Germplasm Collections Identifies a New Velarivirus and Extends the Geographical Spread of Three Other Pear Viruses |
| title_sort | virome scanning of pear germplasm collections identifies a new velarivirus and extends the geographical spread of three other pear viruses |
| topic | apple rubbery wood virus 1 apple rubbery wood virus 2 citrus virus A high-throughput sequencing pear plant virus |
| url | https://apsjournals.apsnet.org/doi/10.1094/PBIOMES-03-24-0030-FI |
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