Complete nucleotide sequence of the cucumber necrosis virus genome

Rochon, D’Ann; Tremaine, J. H.

doi:10.1016/0042-6822(89)90150-5

Cited by 84 publications

(47 citation statements)

References 41 publications

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“…The sequences were from Hillman et al (1989) (TBSV), Tavazza et al (1989) (artichoke mottled crinkle virus, AMCV), Grieco et al (1989) (cymbidium ringspot virus, CyRSV), Rochon & Tremaine (1989) Computer-assisted sequence analysis. Initial comparisons were by the program DOTHELIX which is a version of a diagonal comparison plot generating a full local similarity map and allowing precise determination of the lengths of similar segments (Brodsky et al, 1991).…”

Section: Methodsmentioning

confidence: 99%

Phylogeny of capsid proteins of small icosahedral RNA plant viruses

Dolja

Koonin

1991

Journal of General Virology

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Statistically significant alignment was generated between the amino acid sequences of the (putative) shell (S) domains of the capsid proteins of small RNA plant viruses with icosahedral capsids in the tombusvirus, carmovirus, dianthovirus, sobemovirus and luteovirus groups. Inspection of the alignment showed good correspondence between the experimentally defined fl-strands and ~-helices of the capsid proteins of tomato bushy stunt, southern bean mosaic and turnip crinkle viruses, allowing prediction of the secondary structure elements in proteins with unresolved tertiary structure. It is concluded that this set of viral capsid proteins forms a tight evolutionary cluster. Comparison of the alignment of the proteins of this family with the sequences of other capsid proteins of icosahedral RNA viruses revealed more distant similarities to the satellites of tobacco necrosis, panicum mosaic, tobacco mosaic and maize white line mosaic viruses, as well as to nepo-and comoviruses. The tentative phylogenetic tree derived from the capsid protein alignment separated into three main lineages: (l) carmo-, tombus-and dianthoviruses, (II) southern bean mosaic, tobacco necrosis and maize chlorotic mottle viruses, and (III) luteoviruses. Comparison of this tree topology with the tentative evolutionary schemes for the respective virus RNA-dependent RNA polymerases suggested that gene shuffling is the universal trend in the evolution of small RNA plant virus genomes.

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Section: Methodsmentioning

confidence: 99%

Phylogeny of capsid proteins of small icosahedral RNA plant viruses

Dolja

Koonin

1991

Journal of General Virology

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“…A primer extension reaction using AMV RT (Sambrook et al, 1989) with oligo(dT)l 2 is was performed. RNA isolated from cassava common mosaic potexvirus (CCMV; Costa et al, 1972) was used as a positive control.…”

Section: Characterization Of Rymv Cp and Rnamentioning

confidence: 99%

“…Approx. 45 bacterial colonies were selected following transformation and were screened by hybridization (Sambrook et al, 1989). The probes used for this purpose were either [e-3~P]dCTPqabelled first strand cDNA from RYMV genomic RNA or an c~-32p-end-labelled 20-mer degenerate oligonucleotide deduced from sequencing the N-terminal amino acids of RYMV coat protein (CP).…”

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confidence: 99%

“…Plasmids were prepared by centrifugation in CsC1 (Sambrook et al, 1989), or by a 'miniprep' method that included phenol-chloroform extraction (Serghini et al, 1989). Magic Maxiprep DNA preparation kits purchased from Promega were also used.…”

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confidence: 99%

“…The oligonucleotide used to synthesize the second strand cDNA of the 5' terminus of the RNA was the anchor primer provided by the manufacturer (BRL). After PCR amplification, the products were ethanol-precipitated (Sambrook et al, 1989), digested with suitable restriction enzymes and inserted into the plasmid pBS(KS). Cloned cDNAs were screened for insert size by digestion with the corresponding enzymes.…”

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confidence: 99%

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Nucleotide sequence and genome characterization of rice yellow mottle virus RNA

Yassi

Ritzenthaler

Brugidou

et al. 1994

Journal of General Virology

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Deletion Analysis of the Promoter for the Cucumber Necrosis Virus 0.9-kb Subgenomic RNA

Johnston

Rochon

1995

Virology

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Sequences comprising the core promoter for the cucumber necrosis virus (CNV) 0.9-kb subgenomic RNA have been determined using deletion analysis and site-directed mutagenesis. The deletion studies indicate that the promoter lies within a region located 20 nucleotides upstream and 6 nucleotides downstream and including the subgenomic start site. Sequences further upstream or downstream of the core promoter do not appear to strongly affect promoter activity or viral RNA accumulation. Results of site-directed mutagenesis studies indicate that nucleotides immediately surrounding the subgenomic start site regulate promoter activity. Comparison of sequences within the CNV promoter region with the corresponding region of other tombusviruses shows that the tombusvirus promoter shares a region of near complete identity in 14 of the 26 core promoter nucleotides. Little similarity exists between the CNV 0.9-kb subgenomic RNA promoter and the region surrounding the transcription initiation site for the CNV 2.1-kb subgenomic RNA. Likewise, limited similarity occurs with the 5' region of CNV genomic RNA. Sequences similar to the ICR2-like motifs found in the promoters of several alphavirus-like (supergroup III) plant and animal viruses are not apparent. This study represents the first analysis of a subgenomic promoter from a member of supergroup II of positive-strand RNA viruses.

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Complete nucleotide sequence of the cucumber necrosis virus genome

Cited by 84 publications

References 41 publications

Phylogeny of capsid proteins of small icosahedral RNA plant viruses

Phylogeny of capsid proteins of small icosahedral RNA plant viruses

Nucleotide sequence and genome characterization of rice yellow mottle virus RNA

Deletion Analysis of the Promoter for the Cucumber Necrosis Virus 0.9-kb Subgenomic RNA

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