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Reassessing species demarcation criteria in viroid taxonomy by pairwise identity matrices

hal.structure.identifierCNR Istituto per la Protezione Sostenibile delle Piante [Torino, Italia] [IPSP]
dc.contributor.authorCHIUMENTI, Michela
hal.structure.identifierCNR Istituto per la Protezione Sostenibile delle Piante [Torino, Italia] [IPSP]
dc.contributor.authorNAVARRO, Beatriz
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorCANDRESSE, Thierry
hal.structure.identifierInstituto de Biologia Molecular y Celular de Plantas [IBMCP]
dc.contributor.authorFLORES, Ricardo
hal.structure.identifierCNR Istituto per la Protezione Sostenibile delle Piante [Torino, Italia] [IPSP]
dc.contributor.authorDI SERIO, Francesco
hal.structure.identifierCNR Istituto per la Protezione Sostenibile delle Piante [Torino, Italia] [IPSP]
dc.contributor.authorSERIO, Francesco
dc.date.issued2021
dc.description.abstractEnWith a small, circular and non-protein coding RNA genome, viroids are the smallest infectious agents. They invade plants, which in turn may develop symptoms. Since their discovery about 50 years ago, more than thirty viroids have been reported and classified using as species demarcation less than 90 per cent sequence identity on the overall genome and evidence of biological divergence with respect to the closest related viroids. In the last few years, new viroids have been identified that infect latently their (frequently) woody hosts and have a narrow experimental hosts range, complicating and slowing down studies on their biology. As a consequence, several viroids are still waiting for classification. Moreover, the number of new viroids is expected to increase in the next years due to the use of high-throughput sequencing technologies with diagnostics purposes. Therefore, establishment of reliable species demarcation criteria mainly based on molecular features of viroids is needed. Here, viroid classification is reassessed and a scheme based on pairwise sequence identity matrices is developed. After identifying a threshold pairwise identity score (PWIS) for each viroid genus, to be used as a species demarcation criterion, we show that most of those yet unclassified viroids can be assigned to a known or to a new species, thus limiting the need for additional biological evidence to only a few more complex situations. The advantages of this PWIS-based method are that the proposed identity thresholds for species demarcations are not arbitrarily established and evidence for biological divergence is not mandatory. Importantly, the current classification is not essentially modified. A protocol for a tentative fast classification of new viroids according to the proposed approach is also provided.
dc.language.isoen
dc.publisherOxford University Press
dc.rights.urihttp://creativecommons.org/licenses/by/
dc.subjectVirologie végétale
dc.subjectPathologie végétale
dc.subject.enviroid classification
dc.subject.enpairwise identity threshold
dc.subject.enviroid species
dc.title.enReassessing species demarcation criteria in viroid taxonomy by pairwise identity matrices
dc.typeArticle de revue
dc.identifier.doi10.1093/ve/veab001
dc.subject.halSciences du Vivant [q-bio]
dc.subject.halSciences du Vivant [q-bio]/Biologie végétale
dc.subject.halSciences du Vivant [q-bio]/Biologie végétale/Phytopathologie et phytopharmacie
bordeaux.journalVirus Evolution
bordeaux.pageveab001
bordeaux.volume7
bordeaux.issue1
bordeaux.peerReviewedoui
hal.identifierhal-03152346
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-03152346v1
bordeaux.COinSctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=Virus%20Evolution&rft.date=2021&rft.volume=7&rft.issue=1&rft.spage=veab001&rft.epage=veab001&rft.au=CHIUMENTI,%20Michela&NAVARRO,%20Beatriz&CANDRESSE,%20Thierry&FLORES,%20Ricardo&DI%20SERIO,%20Francesco&rft.genre=article


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