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Title: Complete nucleotide sequence of Nootka lupine vein-clearing virus

Author
item Robertson, Nancy
item COTE, FABIEN - CENTRE DE RECHERCHE-QUEBE
item PARE, CHRISTINE - CENTRE DE RECHERCHE-QUEBE
item LEBLANC, ERIC - CENTRE DE RECHERCHE-QUEBE
item BERGERON, MICHEL - CENTRE DE RECHERCHE-QUEBE
item LECLERC, DENIS - CENTRE DE RECHERCHE-QUEBE

Submitted to: Virus Genes
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/3/2007
Publication Date: 12/20/2007
Citation: Robertson, N.L., Cote, F., Pare, C., Leblanc, E., Bergeron, M., Leclerc, D. 2007. Complete nucleotide sequence of Nootka lupine vein-clearing virus. Virus Genes. 35(3):807-814.

Interpretive Summary: A new plant virus of a native lupine plant (Lupinus nootkatensis) growing in the Talkeetna Mountains of Alaska was reported in 2004. Based on biological and physiochemical properties of the virus, it was named Nootka lupine vein-clearing virus (NLVCV) and tentatively classified in the genus Carmovirus, family Tombusviridae. Genomic sequence data was needed to definitively ascertain its taxonomic placement and phylogenetically compare it with other known disease causing viruses. The whole genome was sequenced to 4142 nucleotides with a similar genetic organization to members in the genus Carmovirus. Phylogenetic analysis of sequence data from the polymerase and coat protein genes determined that NLVCV was most similar to four other carmoviruses: Angelonia flower break virus, Carnation mottle virus, Pelargonium flower break virus, and Saguaro cactus virus. This research significantly impacts the taxonomical placement of a new virus and contributes to the growing number of viruses found in natural ecosystems.

Technical Abstract: The complete genome sequence of Nootka lupine vein-clearing virus (NLVCV) was determined to be 4,172 nucleotides in length containing four open reading frames ORFs with a similar genetic organization and conceptual translations of virus species in the genus Carmovirus, family Tombusviridae. The order and gene product size, starting near the 5'-proximal ORF consisted of the following groups of proteins: 1) polymerase/replicase gene, ORF1 (p27) and ORF1RT (readthrough) (p87), 2) movement proteins ORF2 (p7) and ORF3 (p9), and, 3) the 3'-proximal coat protein ORF4, (p37). The genomic 5'- and 3'-proximal termini contained a short (59 nt) and a relatively longer 406 nt untranslated region, respectively. The longer replicase gene product contained the GDD motif common to all viruses with a RNA-dependent RNA polymerase replication strategy. Phylogenetically, NLVCV formed a subgroup with the following four carmoviruses when separately comparing the amino acids of the coat protein or replicase protein: Carnation mottle virus, Saguaro cactus virus, Angelonia flower break virus, and Pelargonium flower break virus. Based on the given evidence we have concluded that NLVCV should be classified as a distinct species in the genus Carmovirus, family Tombusviridae.