Rudbeckia flower distortion virus (RuFDV) is an unclassified plant pararetrovirus found in Rudbeckia ornamental plants species (a genus of herbaceous perennial plants belonging to Asteraceae family) and proposed to be a tentative new Caulimovirus member (Lockhart and Olszewsk 2009, unpublished) of the Caulimoviridae family (International Committee on the Taxonomy of Viruses -ICTV- Fauquet et al. 2005).This is a perspective clearly supported by phylogenetic analyses inferred based on the COAT(GAG) and pol protein domains (Llorens et al 2009).

The RuFDV virion encapsidates a genomic circular double-stranded DNA molecule of 8222 bp long. The genome encode for seven Open reading frames (ORFs) designated as gp1, gp2, gp3, gp4, gp5, gp6, gp7 whose sequence, size, and organization are similar to those of caulimoviruses (Lockhart and Olszewsk 2009, unpublished). Our sequence analyses show that ORF-gp3 does not reveal significant similarities with the "virion associated protein" (VAP)-ORF III of the other Caulimoviridae species. It is more similar to those of the soymoviruses ORFs C (SbCMV, BRRV and CmYLCV) whose function is still unclear. The sequences of the other protein products show similarities with those encoded by the corresponding ORFs of known caulimoviruses. ORF-gp2 encodes the putative movement protein (MOV), while ORF-gp4 contains the "RNA-binding" motif characteristic of the Caulimoviridae COAT(gag)-like domain (C-X-C-X2-C-X4-H-X4-C ) (Hull 1996; Bouhida et al. 1993; Llorens et al 2009). ORF-gp5 product is a pol polyprotein displaying the typical -aspartic protease (PR), reverse transcriptase (RT) and RNase H (RH) domains, and ORF-gp6 encodes for a translational transactivator protein (TAV) (Lockhart and Olszewsk 2009, unpublished). ORF-gp1 and –gp7 functions remain unknown. ORF-gp6 (TAV) and ORF-gp7 are separated from an intergenic region (850 bp long) as also observed in the genome of several soymoviruses such as SbCMV. In contrast to the other Caulimoviruses, between the ORFs-gp2 (MOV) and -gp3 the genome of RuFDV apparently does not encode for any ORF associated to the "aphid transmission factor" (ATF).



Figure not to scale. If present, long terminal repeats (LTRs) have been highlighted in blue. Amino acid motifs noted with lines indicate the conserved residues in each protein domain, abbreviations below mean:

MA=matrix PR=protease DU or DUT=dUTPase TM=transmembrane TAV or IBMP=transactivator/viroplasmin or inclusion body matrix protein
CA=capsid RT=reverse transcriptase INT=Integrase CHR=chromodomain
NC=nucleocapsid RH=RNaseH SU=surface MOV=movement protein
PPT=polypurine tract PBS=primer binding site ATF=aphid transmission factor VAP=virion associated protein

Related literature

Genbank accession: 221048143
Clade: '
Cluster or genus: Caulimovirus
Branch or class: Class 1
Family: Caulimoviridae
System: LTR retroelements
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Rudbeckia hirta
Wikipedia, courtesy of "Greschtester"
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Welcome to the Gypsy Database (GyDB) an open editable database about the evolutionary relationship of viruses, mobile genetic elements (MGEs) and the genomic repeats where we invite all authors to contribute with their knowledge to improve and expand the topics.
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Llorens, C., Futami, R., Covelli, L., Dominguez-Escriba, L., Viu, J.M., Tamarit, D., Aguilar-Rodriguez, J. Vicente-Ripolles, M., Fuster, G., Bernet, G.P., Maumus, F., Munoz-Pomer, A., Sempere, J.M., LaTorre, A., Moya, A. (2011) The Gypsy Database (GyDB) of Mobile Genetic Elements: Release 2.0 Nucleic Acids Research (NARESE) 39 (suppl 1): D70-D74 doi: 10.1093/nar/gkq1061

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