Harnessing the power of comparative genomics to support the distinction of sister species within Phyllosticta and development of highly specific detection of Phyllosticta citricarpa causing citrus black spot by real-time PCR
Citrus crops are affected by many fungal diseases. Among them, Citrus Black Spot caused by the ascomycete Phyllosticta citricarpa is particularly economically damaging wherever it occurs. Many other species of Phyllosticta are described on Citrus, but only P. citricarpa is considered a quarantine pe...
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| Format: | Article |
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PeerJ Inc.
2023-10-01
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| Online Access: | https://peerj.com/articles/16354.pdf |
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| author | Renaud Ioos Alexandra Puertolas Camille Renault Aida Ndiaye Isabelle Cerf-Wendling Jacqueline Hubert Wen Wang Chen Jiao Hongye Li Josep Armengol Jaime Aguayo |
| author_facet | Renaud Ioos Alexandra Puertolas Camille Renault Aida Ndiaye Isabelle Cerf-Wendling Jacqueline Hubert Wen Wang Chen Jiao Hongye Li Josep Armengol Jaime Aguayo |
| author_sort | Renaud Ioos |
| collection | DOAJ |
| description | Citrus crops are affected by many fungal diseases. Among them, Citrus Black Spot caused by the ascomycete Phyllosticta citricarpa is particularly economically damaging wherever it occurs. Many other species of Phyllosticta are described on Citrus, but only P. citricarpa is considered a quarantine pest on the European continent. In order to prevent the introduction of this species into Europe, it is essential to have a detection test which can reliably identify it, and not confuse it with other species present on citrus, notably P. paracitricarpa. The latter taxon has recently been described as very close to P. citricarpa, and most detection tests do not allow to distinguish the two species. In this work, we exploited the genomic data of 37 isolates of Phyllosticta spp. from citrus, firstly to assess their phylogenetic relationships, and secondly to search for genomic regions that allowed the definition of species-specific markers of P. citricarpa. Analysis of 51 concatenated genes separated P. citricarpa and P. paracitricarpa in two phylogenetic clades. A locus was selected to define a hydrolysis probe and primers combination that could be used in real-time PCR for the specific detection of the quarantine species, to the exclusion of all others present on Citrus. This test was then thoroughly validated on a set of strains covering a wide geographical diversity, and on numerous biological samples to demonstrate its reliability for regulatory control. The validation data highlighted the need to check the reliability of the test in advance, when a change of reagents was being considered. |
| first_indexed | 2024-03-09T07:02:41Z |
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| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T07:02:41Z |
| publishDate | 2023-10-01 |
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| spelling | doaj.art-e8cd24e0439f47de917f982c2b3c110f2023-12-03T09:48:45ZengPeerJ Inc.PeerJ2167-83592023-10-0111e1635410.7717/peerj.16354Harnessing the power of comparative genomics to support the distinction of sister species within Phyllosticta and development of highly specific detection of Phyllosticta citricarpa causing citrus black spot by real-time PCRRenaud Ioos0Alexandra Puertolas1Camille Renault2Aida Ndiaye3Isabelle Cerf-Wendling4Jacqueline Hubert5Wen Wang6Chen Jiao7Hongye Li8Josep Armengol9Jaime Aguayo10Laboratoire de la Santé des Végétaux, Unité de Mycologie, USC INRAE, ANSES, Malzéville, FranceLaboratoire de la Santé des Végétaux, Unité de Mycologie, USC INRAE, ANSES, Malzéville, FranceLaboratoire de la Santé des Végétaux, Unité de Mycologie, USC INRAE, ANSES, Malzéville, FranceLaboratoire de la Santé des Végétaux, Unité de Mycologie, USC INRAE, ANSES, Malzéville, FranceLaboratoire de la Santé des Végétaux, Unité de Mycologie, USC INRAE, ANSES, Malzéville, FranceLaboratoire de la Santé des Végétaux, Unité de Mycologie, USC INRAE, ANSES, Malzéville, FranceThe Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Zhejiang, Hangzhou, ChinaThe Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Zhejiang, Hangzhou, ChinaThe Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Zhejiang, Hangzhou, ChinaInstituto Agroforestal Mediterráneo, Universitat Politècnica de València, Valencia, SpainLaboratoire de la Santé des Végétaux, Unité de Mycologie, USC INRAE, ANSES, Malzéville, FranceCitrus crops are affected by many fungal diseases. Among them, Citrus Black Spot caused by the ascomycete Phyllosticta citricarpa is particularly economically damaging wherever it occurs. Many other species of Phyllosticta are described on Citrus, but only P. citricarpa is considered a quarantine pest on the European continent. In order to prevent the introduction of this species into Europe, it is essential to have a detection test which can reliably identify it, and not confuse it with other species present on citrus, notably P. paracitricarpa. The latter taxon has recently been described as very close to P. citricarpa, and most detection tests do not allow to distinguish the two species. In this work, we exploited the genomic data of 37 isolates of Phyllosticta spp. from citrus, firstly to assess their phylogenetic relationships, and secondly to search for genomic regions that allowed the definition of species-specific markers of P. citricarpa. Analysis of 51 concatenated genes separated P. citricarpa and P. paracitricarpa in two phylogenetic clades. A locus was selected to define a hydrolysis probe and primers combination that could be used in real-time PCR for the specific detection of the quarantine species, to the exclusion of all others present on Citrus. This test was then thoroughly validated on a set of strains covering a wide geographical diversity, and on numerous biological samples to demonstrate its reliability for regulatory control. The validation data highlighted the need to check the reliability of the test in advance, when a change of reagents was being considered.https://peerj.com/articles/16354.pdfDetectionPlant diseaseQuarantineValidationComparative genomicsFungus |
| spellingShingle | Renaud Ioos Alexandra Puertolas Camille Renault Aida Ndiaye Isabelle Cerf-Wendling Jacqueline Hubert Wen Wang Chen Jiao Hongye Li Josep Armengol Jaime Aguayo Harnessing the power of comparative genomics to support the distinction of sister species within Phyllosticta and development of highly specific detection of Phyllosticta citricarpa causing citrus black spot by real-time PCR PeerJ Detection Plant disease Quarantine Validation Comparative genomics Fungus |
| title | Harnessing the power of comparative genomics to support the distinction of sister species within Phyllosticta and development of highly specific detection of Phyllosticta citricarpa causing citrus black spot by real-time PCR |
| title_full | Harnessing the power of comparative genomics to support the distinction of sister species within Phyllosticta and development of highly specific detection of Phyllosticta citricarpa causing citrus black spot by real-time PCR |
| title_fullStr | Harnessing the power of comparative genomics to support the distinction of sister species within Phyllosticta and development of highly specific detection of Phyllosticta citricarpa causing citrus black spot by real-time PCR |
| title_full_unstemmed | Harnessing the power of comparative genomics to support the distinction of sister species within Phyllosticta and development of highly specific detection of Phyllosticta citricarpa causing citrus black spot by real-time PCR |
| title_short | Harnessing the power of comparative genomics to support the distinction of sister species within Phyllosticta and development of highly specific detection of Phyllosticta citricarpa causing citrus black spot by real-time PCR |
| title_sort | harnessing the power of comparative genomics to support the distinction of sister species within phyllosticta and development of highly specific detection of phyllosticta citricarpa causing citrus black spot by real time pcr |
| topic | Detection Plant disease Quarantine Validation Comparative genomics Fungus |
| url | https://peerj.com/articles/16354.pdf |
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