Complete Nucleotide Sequence and Genome Organization of Calibrachoa Mottle Virus (CbMV) - a new Species in the Genus Carmovirus, Family Tombusviridae.

Authors: Gulati Sakhuja, Anju; Liu, Hsing Yeh

Submitted to: Virus Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/8/2009
Publication Date: 2/1/2010
Citation: Gulati Sakhuja, A.N., Liu, H. 2010. Complete Nucleotide Sequence and Genome Organization of Calibrachoa Mottle Virus (CbMV) - a new Species in the Genus Carmovirus, Family Tombusviridae. Virus Research. 147:216-223.

Interpretive Summary: Calibrachoa mottle virus (CbMV) infects Calibrachoa, an important new horticultural plant both in Europe and the United States. The virus has isometric particles of approximately 29-31nm in diameter. The most evident symptoms are leaf mottling, chlorotic blotch and interveinal yellowing. The virus is transmitted by mechanical inoculations, but not transmitted by aphids or whiteflies. The cDNA clones were prepared by using either virions purified from infected Nicotiana benthamiana tissues or dsRNA extracted from infected Calibrachoa plant tissues. Complete genomic sequence of the viral RNA has been determined. The CbMV genome has a positive-sense single stranded RNA, 3919 nucleotides in length, examination of which indicated five open reading frames (ORFs). A comparison of amino acid sequences of the ORFs of CbMV with members of Tombusviridae shows that CbMV is closely related to members of genus Carmovirus. The whole genome nucleotide analysis (% identity) among other carmoviruses and CbMV reveals a similar pattern. Therefore, the genome organization, physicochemical properties, sequence alignments and phylogenetic analysis support the classification of CbMV in the genus Carmovirus, family Tombusviridae.

Technical Abstract: Calibrachoa mottle virus (CbMV) infects Calibrachoa, an important new horticultural plant both in Europe and the United States. The virus has isometric particles of approximately 29-31nm in diameter. The most evident symptoms are leaf mottling, chlorotic blotch and interveinal yellowing. The virus is transmitted by mechanical inoculations, but not transmitted by aphids or whiteflies. The cDNA clones were prepared by using either virions purified from infected Nicotiana benthamiana tissues or dsRNA extracted from infected Calibrachoa plant tissues. Complete genomic sequence of the viral RNA has been determined. The CbMV genome has a positive-sense single stranded RNA, 3919 nucleotides in length, examination of which indicated five open reading frames (ORFs). The first ORF initiating near the 5' terminus (ORF1) encodes a protein with predicted molecular weight of 28,123 Da (p28). ORF2 extends through the amber stop codon of ORF1 to give a protein with a predicted molecular weight of 87,073 Da (p87). The readthrough domain of p87 contains the GDD motif common to RNA-dependent RNA polymerases. ORF3 and ORF4 encode two small overlapping polypeptides of 7689 Da (p8) and 9275 Da (p9), respectively. The 3'-proximal ORF5 encodes the capsid protein of 37,182 Da (p37). The untranslated 5'- and 3'-terminus are composed of 34 and 234 non-coding nucleotides, respectively. A comparison of amino acid sequences of the ORFs of CbMV with members of Tombusviridae shows that CbMV is closely related to members of genus Carmovirus. Phylogenetic analysis reveals that CbMV forms a subgroup with Angelonia flower break virus (AnFBV), Carnation mottle virus (CarMV), Nootka lupine vein-clearing virus (NLVCV), Pelargonium flower break virus (PFBV) Pelargonium line pattern virus (PLPV) and Saguaro cactus virus (SCV), when the amino acids of coat protein and replicase protein are compared separately. The whole genome nucleotide analysis (% identity) among other carmoviruses and CbMV reveals a similar pattern. Therefore, the genome organization, physicochemical properties, sequence alignments and phylogenetic analysis support the classification of CbMV in the genus Carmovirus, family Tombusviridae.