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Reassessment of the Columnea latent viroid (CLVd) Taxonomic Classification

Columnea latent viroid (CLVd) is a member of the Pospiviroid family and its naked circular RNA genome typically forms native “rod-like” secondary structures. In this work, the CLVd taxonomy was reevaluated based on sequence similarity and phylogenetic analysis, as well as the evaluation of the sympt...

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Autores principales: Tangkanchanapas, Parichate, Haegeman, Annelies, Höfte, Monica, De Jonghe, Kris
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8224301/
https://www.ncbi.nlm.nih.gov/pubmed/34064131
http://dx.doi.org/10.3390/microorganisms9061117
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author Tangkanchanapas, Parichate
Haegeman, Annelies
Höfte, Monica
De Jonghe, Kris
author_facet Tangkanchanapas, Parichate
Haegeman, Annelies
Höfte, Monica
De Jonghe, Kris
author_sort Tangkanchanapas, Parichate
collection PubMed
description Columnea latent viroid (CLVd) is a member of the Pospiviroid family and its naked circular RNA genome typically forms native “rod-like” secondary structures. In this work, the CLVd taxonomy was reevaluated based on sequence similarity and phylogenetic analysis, as well as the evaluation of the symptom development and disease severity of four selected CLVd isolates in a range of host species. The phylogenetic analysis showed that all CLVd isolates were clustered into five distinct clades: (I) severe isolates originally found in tomato crops in Thailand, (II) ornamental isolates, (III) mild isolates originally found in tomato crops in Thailand, and two clades (IV and V) containing mild isolates originating mainly from tomato crops in European countries, with different virulence levels on several hosts. Our analysis demonstrated that some CLVd isolates have a sequence similarity of less than 90% within the species taxon, as well as distinct biological characteristics (symptom development and virulence), both of which are important ICTV criteria for viroid classification. For these reasons, we propose that CLVd should be re-classified into at least three main taxonomic lineages: a “CLVd-tomato Asian lineage” (I), a “CLVd-tomato European lineage” (IV) and a “CLVd-ornamental European lineage” (II), plus two minor lineages (III and V), fitting the ICTV criteria.
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spelling pubmed-82243012021-06-25 Reassessment of the Columnea latent viroid (CLVd) Taxonomic Classification Tangkanchanapas, Parichate Haegeman, Annelies Höfte, Monica De Jonghe, Kris Microorganisms Article Columnea latent viroid (CLVd) is a member of the Pospiviroid family and its naked circular RNA genome typically forms native “rod-like” secondary structures. In this work, the CLVd taxonomy was reevaluated based on sequence similarity and phylogenetic analysis, as well as the evaluation of the symptom development and disease severity of four selected CLVd isolates in a range of host species. The phylogenetic analysis showed that all CLVd isolates were clustered into five distinct clades: (I) severe isolates originally found in tomato crops in Thailand, (II) ornamental isolates, (III) mild isolates originally found in tomato crops in Thailand, and two clades (IV and V) containing mild isolates originating mainly from tomato crops in European countries, with different virulence levels on several hosts. Our analysis demonstrated that some CLVd isolates have a sequence similarity of less than 90% within the species taxon, as well as distinct biological characteristics (symptom development and virulence), both of which are important ICTV criteria for viroid classification. For these reasons, we propose that CLVd should be re-classified into at least three main taxonomic lineages: a “CLVd-tomato Asian lineage” (I), a “CLVd-tomato European lineage” (IV) and a “CLVd-ornamental European lineage” (II), plus two minor lineages (III and V), fitting the ICTV criteria. MDPI 2021-05-21 /pmc/articles/PMC8224301/ /pubmed/34064131 http://dx.doi.org/10.3390/microorganisms9061117 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Tangkanchanapas, Parichate
Haegeman, Annelies
Höfte, Monica
De Jonghe, Kris
Reassessment of the Columnea latent viroid (CLVd) Taxonomic Classification
title Reassessment of the Columnea latent viroid (CLVd) Taxonomic Classification
title_full Reassessment of the Columnea latent viroid (CLVd) Taxonomic Classification
title_fullStr Reassessment of the Columnea latent viroid (CLVd) Taxonomic Classification
title_full_unstemmed Reassessment of the Columnea latent viroid (CLVd) Taxonomic Classification
title_short Reassessment of the Columnea latent viroid (CLVd) Taxonomic Classification
title_sort reassessment of the columnea latent viroid (clvd) taxonomic classification
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8224301/
https://www.ncbi.nlm.nih.gov/pubmed/34064131
http://dx.doi.org/10.3390/microorganisms9061117
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