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Geminivirus Strain Demarcation and Nomenclature

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dc.creator Moriones, E.
dc.date 2008-05-28T06:57:06Z
dc.date 2008-05-28T06:57:06Z
dc.date 2008-04-04
dc.date.accessioned 2017-01-31T01:29:01Z
dc.date.available 2017-01-31T01:29:01Z
dc.identifier http://hdl.handle.net/10261/4593
dc.identifier 10.1007/s00705-008-0037-6
dc.identifier.uri http://dspace.mediu.edu.my:8181/xmlui/handle/10261/4593
dc.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.
dc.description 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, China
dc.description Peer reviewed
dc.format 1437759 bytes
dc.format application/pdf
dc.language eng
dc.publisher Springer
dc.relation Virologia. Enrique
dc.relation 3
dc.rights openAccess
dc.title Geminivirus Strain Demarcation and Nomenclature
dc.type Artículo

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