Reassessing species demarcation criteria in viroid taxonomy by pairwise identity matrices
| Autor: | Chiumenti, Michela, Navarro, Beatriz, Candresse, Thierry, Flores, Ricardo, Di Serio, Francesco, Serio, Francesco |
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| Přispěvatelé: | Istituto per la Protezione Sostenibile delle Piante (CNR), Biologie du fruit et pathologie (BFP), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Bordeaux (UB), Instituto de Biologia Molecular y Celular de Plantas, Universitat de València (UV), This project has been partially funded from the European Union’s Horizon 2020 Research and Innovation Program under the Marie Skłodowska-Curie grant agreement no.734736. |
| Jazyk: | angličtina |
| Rok vydání: | 2021 |
| Předmět: |
Viroid
viruses [SDV]Life Sciences [q-bio] Identity matrix Virologie végétale Pathologie végétale Microbiology Genome 03 medical and health sciences Reflections Genus Virology Taxonomy (general) Identity score [SDV.BV]Life Sciences [q-bio]/Vegetal Biology AcademicSubjects/MED00860 pairwise identity threshold 030304 developmental biology 0303 health sciences biology 030306 microbiology AcademicSubjects/SCI01130 AcademicSubjects/SCI02285 viroid species biology.organism_classification [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy viroid classification pairwise identity threshold viroid species Evolutionary biology viroid classification Identity (object-oriented programming) Pairwise comparison |
| Zdroj: | Virus Evolution Virus Evolution, Oxford University Press, 2021, 7 (1), pp.veab001. ⟨10.1093/ve/veab001⟩ |
| ISSN: | 2057-1577 |
| Popis: | With 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. |
| Databáze: | OpenAIRE |
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