Geminivirus Strain Demarcation and Nomenclature

Geminivirus taxonomy and nomenclature is growing in complexity with the number of genomic sequences deposited in sequence databases. Taxonomic and nomenclatural updates are published at regular intervals (Fauquet et al. in Arch Virol 145:1743–1761, 2000, Arch Virol 148:405–421, 2003). A system to st...

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Author: Moriones, Enrique
Format: article
Publication Date:2008
Country:España
Institution:Consejo Superior de Investigaciones Científicas (CSIC)
Repository:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/4593
Online Access:http://hdl.handle.net/10261/4593
Access Level:Open access
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spelling Geminivirus Strain Demarcation and NomenclatureMoriones, EnriqueGeminivirus taxonomy and nomenclature is growing in complexity with the number of genomic sequences deposited in sequence databases. Taxonomic and nomenclatural updates are published at regular intervals (Fauquet et al. in Arch Virol 145:1743–1761, 2000, Arch Virol 148:405–421, 2003). A system to standardize virus names, and corresponding guidelines, has been proposed (Fauquet et al. in Arch Virol 145:1743–1761, 2000). This system is now followed by a large number of geminivirologists in the world, making geminivirus nomenclature more transparent and useful. In 2003, due to difficulties inherent in species identification, the ICTV Geminiviridae Study Group proposed new species demarcation criteria, the most important of which being an 89% nucleotide (nt) identity threshold between full-length DNA-A component nucleotide sequences for begomovirus species. This threshold has been utilised since with general satisfaction. More recently, an article has been published to clarify the terminology used to describe virus entities below the species level [5]. The present publication is proposing demarcation criteria and guidelines to classify and name geminiviruses below the species level. Using the Clustal V algorithm (DNAStar MegAlign software), the distribution of pairwise sequence comparisons, for pairs of sequences below the species taxonomic level, identified two peaks: one at 85–94% nt identity that is proposed to correspond to ‘‘strain’’ comparisons and one at 92–100% identity that corresponds to ‘‘variant’’ comparisons. Guidelines for descriptors for each of these levels are proposed to standardize nomenclature under the species level. In this publication we review the status of geminivirus species and strain demarcation as well as providing updated isolate descriptors for a total of 672 begomovirus isolates. As a consequence, we have revised the status of some virus isolates to classify them as ‘‘strains’’, whereas several others previously classified as ‘‘strains’’ have been upgraded to ‘‘species’’. In all other respects, the classification system has remained robust, and we therefore propose to continue using it. An updated list of all geminivirus isolates and a phylogenetic tree with one representative isolate per species are provided.Estacio´n Experimental ‘‘La Mayora’’, Consejo Superior de Investigaciones Cientı´ficas, 29750 Algarrobo-Costa, Ma´laga, Spain ILTAB/Danforth Plant Science Centre, 975 N. Warson Rd., St Louis, MO 63132, USA e-mail: cmf@danforthcenter.org; iltab@danforthcenter.org URL: www.danforthcenter.org/iltab/ National Institute for Biotechnology and Genetic Engineering, Jhang Road, P.O. Box 577, Faisalabad, Pakistan Department of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA John Innes Centre, Colney Lane, Norwich NR4 7UH, UK Departamento de Fitopatologia, Universidade Federal de Vic¸osa, Vic¸osa, MG 36570-000, Brazil Institute of Biotechnology, Zhejiang University, Hangzhou 310029, ChinaPeer reviewedSpringer Nature200820082008info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_65011437759 bytesapplication/pdfhttp://hdl.handle.net/10261/4593reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)InglésVirologia. Enrique3info:eu-repo/semantics/openAccessoai:digital.csic.es:10261/45932026-05-22T06:33:51Z
dc.title.none.fl_str_mv Geminivirus Strain Demarcation and Nomenclature
title Geminivirus Strain Demarcation and Nomenclature
spellingShingle Geminivirus Strain Demarcation and Nomenclature
Moriones, Enrique
title_short Geminivirus Strain Demarcation and Nomenclature
title_full Geminivirus Strain Demarcation and Nomenclature
title_fullStr Geminivirus Strain Demarcation and Nomenclature
title_full_unstemmed Geminivirus Strain Demarcation and Nomenclature
title_sort Geminivirus Strain Demarcation and Nomenclature
dc.creator.none.fl_str_mv Moriones, Enrique
author Moriones, Enrique
author_facet Moriones, Enrique
author_role author
description Geminivirus taxonomy and nomenclature is growing in complexity with the number of genomic sequences deposited in sequence databases. Taxonomic and nomenclatural updates are published at regular intervals (Fauquet et al. in Arch Virol 145:1743–1761, 2000, Arch Virol 148:405–421, 2003). A system to standardize virus names, and corresponding guidelines, has been proposed (Fauquet et al. in Arch Virol 145:1743–1761, 2000). This system is now followed by a large number of geminivirologists in the world, making geminivirus nomenclature more transparent and useful. In 2003, due to difficulties inherent in species identification, the ICTV Geminiviridae Study Group proposed new species demarcation criteria, the most important of which being an 89% nucleotide (nt) identity threshold between full-length DNA-A component nucleotide sequences for begomovirus species. This threshold has been utilised since with general satisfaction. More recently, an article has been published to clarify the terminology used to describe virus entities below the species level [5]. The present publication is proposing demarcation criteria and guidelines to classify and name geminiviruses below the species level. Using the Clustal V algorithm (DNAStar MegAlign software), the distribution of pairwise sequence comparisons, for pairs of sequences below the species taxonomic level, identified two peaks: one at 85–94% nt identity that is proposed to correspond to ‘‘strain’’ comparisons and one at 92–100% identity that corresponds to ‘‘variant’’ comparisons. Guidelines for descriptors for each of these levels are proposed to standardize nomenclature under the species level. In this publication we review the status of geminivirus species and strain demarcation as well as providing updated isolate descriptors for a total of 672 begomovirus isolates. As a consequence, we have revised the status of some virus isolates to classify them as ‘‘strains’’, whereas several others previously classified as ‘‘strains’’ have been upgraded to ‘‘species’’. In all other respects, the classification system has remained robust, and we therefore propose to continue using it. An updated list of all geminivirus isolates and a phylogenetic tree with one representative isolate per species are provided.
publishDate 2008
dc.date.none.fl_str_mv 2008
2008
2008
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
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url http://hdl.handle.net/10261/4593
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Virologia. Enrique
3
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dc.publisher.none.fl_str_mv Springer Nature
publisher.none.fl_str_mv Springer Nature
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instname:Consejo Superior de Investigaciones Científicas (CSIC)
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