Complete sequence of the RNA1 of an isolate of WCCV1, type species of the genus Alphacryptovirus
Arch Virol(2005)150:399–402
DOI10.1007/s00705-004-0422-8
Complete sequence of the RNA1of an isolate
of White clover cryptic virus1,type species
of the genus Alphacryptovirus?
Annotated Sequence Record
G.Boccardo1and T.Candresse2
1Istituto di Virologia Vegetale,CNR,Torino,Italy
2Equipe de Virologie,INRA et Universit′e Bordeaux2,
Villenave d’Ornon,France
Received August16,2004;accepted August16,2004
Published online October21,2004c Springer-Verlag2004
Introduction
Plant cryptic viruses,are intriguing agents very tightly associated with their host plants.They form isometric particles which encapsidate a double stranded RNA(dsRNA)genome with2or3components.Like other members of the Partitiviridae,which include viruses of fungi,they do not seem to cause symptoms in their hosts.They are transmitted by the ovule and by pollen to the seed embryo but there is no graft-transmission and apparently no cell-to-cell transport,except at cell division.The only known mode of transmission is by seed.The cryptic viruses are classi?ed in two genera,Alphacryptovirus and Betacryptovirus,according to differences in particle morphology and size of the genomic dsRNAs[5].White clover cryptic virus1(WCCV1)is the type species of the genus Alphacryptovirus but the sequences of its two genome segments and their encoded proteins have not been published.We here report on these,as regards RNA1;the following paper [2]reports the full sequence of RNA2.
Provenance of the virus material
The WCCV1isolate used was obtained from naturally infected white clover seedlings as described previously[3,4].Viral cDNAs were prepared from puri?ed WCCV1dsRNAs extracted from puri?ed viral particles[3]using the technique of Gubler and Hoffman[6]following oligo-dT priming.5 terminal sequences ?This manuscript is dedicated to the memory of Dr.Guido Boccardo.
400G.Boccardo and T.Candresse
were con?rmed by primer extension on the puri?ed viral dsRNAs.The sequence obtained has been deposited in the Genbank database under accession number AY705784.
Sequence properties
The full-length sequence of the RNA1ofWCCV1was determined from overlaping cDNA clones and shown to be1955nt long,excluding the polyA tail found at the 3 end of the coding strand.The sequence has a G+C%of44.1%,with a marked imbalance in composition since it contains only17.6%G while the three other bases are each represented at26.5–28.5%.The5 non-coding region(NCR)is 74nucleotides long and shows a substantially lower G+C%(36.4%)than the rest of the molecule.There is a single open reading frame ending with a UAA stop codon at positions1923–1925,while the3 NCR is particularly short,being only30nucleotides long(Fig.1).The encoded protein of616amino acids has a calculated molecular weight of72.9kDa and an isoelectric point of7.28.This protein shows signi?cant homologies with the RNA-dependent RNA polymerase (RdRp)of members of the Partitiviridae[5].In keeping with the identi?cation of the RNA1-encoded protein as the viral RdRp,this protein was shown in in vitro immunoprecipitation experiments to be recognized together with the viral CP encoded by the RNA2[2]by an antiserum directed against WCCV1particles (result not shown),which are known to possess an RNA polymerase activity [1].
Surprisingly,database searches and multiple viral RdRp alignments showed that the closest homology of the WCCV1RdRP was with the comparable pro-tein of a fungal Partitivirus from Heterobasidion annosum(AF348136,59.1% identity)while much lower values were observed with the two RdRp sequences available for plant cryptic viruses,that of Beet cryptic virus3[8](JQ2034), another Alphacryptovirus showing only21%identity)and that of a cryptic virus from Pyrus pyrifolia[7](BAA34783,19.7%identity).On the other hand,these two sequences were clearly related to each other,showing52.6%identity.These results are con?rmed by the phylogenetic tree shown in Fig.2,which clearly indicates that the WCCV1RdRp clusters with the homologous protein from members of the genus Partitivirus and away from those of other cryptic viruses. Thus,the RdRp of alphacryptoviruses do not seem to form a phylogenetically coherent ensemble,and re-examination of the taxonomy of these viruses may be warranted.
Fig.1.Schematic representation of the genomic organisation of the WCCV1RNA1encoding the viral RNA-dependent RNA polymerase(RdRp)
WCCV1RNA1sequence401
Fig.2.Phylogenetic tree reconstructed from the amino acid sequences of the RNA-dependent RNA polymerases of members of the family Partitiviridae.The sequence of the H.victoriae 145S virus(a member of the family Totiviridae,highlighted in black)was used as an outgroup. The RdRps of plant cryptic viruses are highlighted in grey.Bootstrap values superior to
70%are shown
Acknowledgements
The help of https://www.wendangku.net/doc/123380751.html,ne(Istituto di Virologia Vegetale,Torino,Italy)for his comments and suggestions for improving this manuscript,and to M.d’Aquilio for her technical assistance to G.B.are gratefully acknowledged.
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Author’s address:Thierry Candresse,Equipe de Virologie,UMR GDPP,IBVM,INRA BP81,33883Villenave d’Ornon Cedex,France;e-mail:tc@bordeaux.inra.fr