The classification and nomenclature of endogenous viruses of the family Caulimoviridae
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The classification and nomenclature of endogenous viruses of the family Caulimoviridae Andrew D. W. Geering • Tanya Scharaschkin Pierre-Yves Teycheney
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Received: 3 July 2009 / Accepted: 3 August 2009 / Published online: 8 November 2009 Ó Springer 2009
Abstract Endogenous members of the family Caulimoviridae have now been found in the genomes of many plant species. Although these sequences are usually fragmented and rearranged and show varying degrees of decay, the genomes of the ancestral viruses can often be reassembled in silico, allowing classification within the existing viral taxonomic framework. In this paper, we describe analyses of endogenous members of the family Caulimoviridae in the genomes of Oryza sativa, Nicotiana tabacum and Solanum spp. and on the basis of phylogeny, genome organization and genetic distance within the pol gene, propose two new virus genera called Orendovirus and Solendovirus. A system of nomenclature for endogenous virus sequences in plants is also proposed.
A. D. W. Geering T. Scharaschkin Cooperative Research Centre for National Plant Biosecurity, Innovation Centre, University Drive, University of Canberra, Bruce, ACT 2617, Australia A. D. W. Geering (&) Queensland Primary Industries and Fisheries, 80 Meiers Road, Indooroopilly, QLD 4068, Australia e-mail: [email protected] T. Scharaschkin School of Natural Resource Sciences, Queensland University of Technology, Brisbane, QLD 4001, Australia P.-Y. Teycheney BIOS-UPR75, Centre de Coope´ration Internationale en Recherche Agronomique pour le De´veloppement, Station de Neufchaˆteau, Sainte-Marie 97130, Capesterre Belle-Eau Guadeloupe, France
Retroelements are genetic entities that occur as both RNA and DNA molecules and alternate between the two through cycles of reverse transcription and transcription. The diversity of viral retroelements is very large and includes retroviruses (family Retroviridae), pararetroviruses (families Caulimoviridae and Hepadnaviridae) and long terminal repeat (LTR) retrotransposons (families Metaviridae and Pseudoviridae) [10, 18]. All viral retroelements contain a gag-pol replicon core, to which is linked additional adaptive genes that enable the different types of retroelement to occupy various ecological niches [17]. The gag gene encodes the major structural protein or capsid protein, and the pol gene encodes an aspartic protease and reverse transcriptase (RT) with RNase H1 activity [10]. The RT has conserved amino acid motifs indicating a common evolutionary origin. Phylogenetic analyses using this part of the protein have led to the development of a universal classification system for retroelements and enabled accurate taxonomic placement, even in the absence of a complete genome sequence [5, 10, 45]. The term ‘endogenous’ is associated with viral retroelements that have infected host germ line cells at some time in the past and are inherited from parent to offspring as provirus in a Mendelian fashion. Within the animal kingdom, endogenous viral retroelements
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