Nucleotide sequence of the genome of an Australian isolate of turnip yellow mosaic tymovirus

The nucleotide sequence of the Club Lake isolate of turnip yellow mosaic virus (TYMV-CL) genomic RNA has been determined. The genome is 6319 nucleotide residues in length and has three major open reading frames (ORFs), two of which overlap. The smallest ORF is proximal to the 3' terminus and encodes the virion protein gene, which has 98% sequence similarity with the virion protein gene reported for the type strain of TYMV. The largest ORF is from nucleotide residues 96 to 5630, and encodes a protein some parts of which show sequence similarities to the possible RNA replicases and nucleotide binding proteins of other viruses. The third ORF is from nucleotide residues 89 to 1975 and overlaps the 5' end of the largest ORF in a manner similar to that found in several animal viral genomes. The function of the protein encoded by this ORF is unknown. The genomes of tymoviruses have, characteristically, an unusually large cytosine content and small guanosine content. This compositional bias is mirrored in the codon and dinucleotide frequencies of the TYMV-CL genome, but is only partially reflected in the amino acid sequences encoded by the genome.     

Nucleotide sequence of the genome of eggplant mosaic tymovirus

The sequence of the RNA genome of an isolate of eggplant mosaic tymovirus from Trinidad (EMV-Trin) has been determined. The genome is 6330 nucleotide residues in length and contains three open reading frames; two overlapping genes, whose initiation codons are separated by seven nucleotide residues (nucleotide residues 102-2051 and 109-5628) near the 5' terminus, and the virion protein gene, which is near the 3' terminus (nucleotide residues 5633-6199). The genomes of EMV-Trin and turnip yellow mosaic tymovirus have the same genomic organization and similar nucleotide and encoded amino acid sequences. The nucleotide residues adjacent to the initiation codons of tymoviral overlapping genes have closely similar sequences which may form a weak stem-loop secondary structure that regulates their translation.     

Virion protein sequence variation among Australian isolatesof turnip yellow mosaic tymovirus

Summary.  The virion protein genes, and 3′ untranslated regions, of six variants of turnip yellow mosaic tymovirus (TYMV) that produced different symptoms in their native host Cardamine robusta and in Chinese cabbage plants, have been sequenced. The sequences have been compared with each other, and with the same region of the pBL-16 clone of the Blue Lake isolate of TYMV. The sequences of the virion protein genes differed by a mean of 1.89% (range 0–2.82%), and the encoded proteins by a mean of 1.71% (range 0–3.17%). The nucleotide differences were confined to the 5′-most 60% of the gene, whereas there were amino acid differences only among residues 12 to 29 and residue 102 (numbered from the N-terminus) of the virion protein involving only hydrophobic residues at the surface of the protein. The amino acid and nucleotide differences between the seven isolates did not correlate with differences in the symptoms they caused, but confirmed earlier estimates of genetic variability in the wild populations of the virus. Accepted August 1, 1997 Received April 3, 1997     

Genetic variation in populations of kennedya yellow mosaic tymovirus

Summary Kennedya yellow mosaic tymovirus (KYMV) occurs along the eastern Australian seaboard in the perennial legumesDesmodium triflorum andD. scorpiurus in the north, andKennedya rubicunda in the south. The genetic variation of more than 100 isolates of KYMV, most of them from the north, has been studied using an RNA hybrid mismatch polymorphism (RHMP) method. The method clearly separated the isolates into two groups; all the northernDesmodium isolates formed one group and all theKennedya isolates from the south another. These sub-populations were themselves variable and theDesmodium population alone was more variable than that of the related turnip yellow mosaic tymovirus in the Kosciusko alpine area.     

RNA hybrid mismatch polymorphisms in Australian populations of turnip yellow mosaic tymovirus

Summary In the Mt. Kosciusko alpine area of Australia there are three well-separated populations ofCardamine lilacina, an endemic sward-forming perennial brassica, and these are infected with turnip yellow mosaic tymovirus. The genetic variation in these viral populations has been assessed by an RNA hybrid mismatch polymorphism method. About 100 isolates were examined; the genomic RNA of each isolate was prepared from a shoot of a single wildC. lilacina plant. RNA hybrid mismatch polymorphisms (RHMPs) were assessed in six regions of the genomes using labelled negative-strand probes transcribed from selected portions of a cloned TYMV genome. The probed region at the 3 end of the genome showed little variation and over 95% of the isolates gave the same pattern. However, other parts of the genome, including the 5 non-coding region, were much more variable. There was no significant correlation between groupings based on the RHMP patterns, and the location from which the isolates were collected, nor with the symptom type or severity shown by their host plants. The patterns of variation suggested that all three populations of the virus are a single quasi-species; at most one tenth of the isolates gave similar RHMP patterns, those of the master copy.     

Nucleotide sequence comparisons of turnip yellow mosaic virus isolates from Australia and Europe

Summary The genomic sequences of four isolates of turnip yellow mosaic virus (TYMV-Cd) from Australia, and three TYMV-1 (type) and three TYMV-2 (cauliflower) isolates from Europe were compared by cDNA-RNA hybridization tests, by analysis of the fragments produced from cDNA-RNA hybrids by restriction endonuclease treatment, and by determining the 3 terminal nucleotide sequences of their coat protein mRNAs. All three methods showed only slight differences (ca. 1%) between the mRNA sequences of different TYMV-1 and TYMV-Cd isolates, and did not distinguish between those groups of isolates. By contrast, the nucleotide sequences of TYMV-2 isolates differed from those of the other TYMVs by ca. 5% (sequence analysis) to 11% (restriction fragment analysis).Published biogeographic evidence has indicated that the TYMV-Cd and TYMV-1 populations probably separated more than 12,000 years ago. This implies that these TYMV genomes have changed at a rate of, at most, 1% in 10,000 years.     

Complete genome sequence of an isolate of Clerodendron yellow mosaic virus--a new begomovirus from India

Clerodendron inerme, a common hedge plant grown in India, is affected by a yellow mosaic disease caused by a begomovirus. In the present study, the complete genome (DNA A) of this virus was cloned and sequenced. The total size of DNA A is 2760 nucleotides. The genome of this virus contains six open reading frames and a non-coding intergenic region of 293 nucleotides. Nucleotide sequence comparison analysis revealed maximum sequence identity with Papaya leaf curl virus-Pakistan [Pakistan:Cotton:2002] (73.9%). As this virus had less than 89% identity with other begomoviruses, it was identified as a new begomovirus species and tentatively, named as Clerodendron yellow mosaic virus-[India:New Delhi:2007] (ClYMV-[IN:ND:07]).     

Complete genome sequence of pepper yellow mosaic virus, a potyvirus, occurring in Brazil

The complete genomic sequence of pepper yellow mosaic virus (PepYMV), a member of the genus Potyvirus, was determined. The sequence was 9745 nucleotides long, excluding the 3' poly(A) tail. The genome contained a large open reading frame encoding a polyprotein of 3085 amino acids, which contained the typically conserved motifs found in members of the genus Potyvirus and an additional P3-PIPO (pretty interesting potyvirus ORF). In a pairwise comparison with other potyvirus sequences, the full genome of PepYMV shared a maximum of 63.84 % nucleotide sequence identity with pepper mottle virus (PepMoV), followed by verbena virus Y (VVY, 62.11 %), potato virus Y (PVY, 62.07 %) and Peru tomato mosaic virus (PTV, 62.00 %). Based upon a phylogenetic analysis, PepYMV was most closely related to PepMoV and PTV, within the PVY subgroup cluster, like most potyviruses isolated in solanaceous hosts in South America.     

Nucleotide sequence of the geminivirus chloris striate mosaic virus

The genome of chloris striate mosaic virus (CSMV) comprises a single circular DNA as determined by analyses on virion single-stranded (ss) DNA and virus-specific covalently closed circular (ccc) DNA isolated from infected plants. The nucleotide sequence of CSMV DNA was determined from cccDNA and the data were accommodated into one DNA circle of 2750 nucleotides. Comparison of the nucleotide sequence with those of maize streak virus (MSV), wheat dwarf virus (WDV), and digitaria streak virus (DSV) showed 49, 47, and 48% DNA homology, respectively. The sequence has four potential open reading frames for proteins of greater than 10,000 mol wt, two in the viral (+) sense and two in the complementary (-) sense. Three of these potential coding regions have homologous counterparts, by comparison of the amino acid sequences, among the open reading frames reported for MSV, WDV, and DSV. CSMV encapasidates primer molecules able to prime the synthesis in vitro of a complementary strand to virion DNA, initiating this reaction at one site on the genome. The CSMV primer comprising approximately 88 nucleotides was located within the smaller of two intergenic or noncoding regions.     

Nucleotide sequence and genome organization of the medium RNA of Iris yellow spot virus from the United States

Iris yellow spot tospovirus (IYSV) of the family Bunyaviridae causes a serious disease in onion in the USA and other parts of the world. Inspite of its economic importance, the complete genomic sequence of IYSV from the USA is not available. The genome structure and organization of the medium (M) RNA of a Washington (WA) isolate of IYSV were determined and compared to the corresponding region of two isolates previously described from Brazil and The Netherlands. Sequence analysis showed that the M-RNA was 4,817 nucleotides long and potentially coded for the movement protein (NSm) in the viral sense and the glycoprotein precursor (Gn and Gc) in the viral complementary sense. The predicted sizes of NSm and Gn/Gc precursor were 34.7 and 128.84 kDa, respectively. The two open reading frames are separated by a 380 nucleotide intergenic region. Phylogenetic analysis of the NSm and Gn/Gc genes from the WA isolate showed grouping that reflected their respective serogroups. The WA isolate formed a close cluster with the two previously reported IYSV isolates and the IYSV cluster was distinguishable from other tospovirus species. This is the first report of complete genomic sequence of the M-RNA of IYSV from the US. Sequences reported here is available in NCBI GenBank under the following accession no.: FJ361359.     

Nucleotide sequence of cucumber mosaic virus-associated RNA 5

The complete nucleotide sequence of cucumber mosaic virus-associated (satellite) RNA 5 (CARNA 5) strain D has been determined. The molecule is 335 residues long and is capped at its 5' extremity. There were minor variations in the sequence of different preparations of the satellite RNA. Otherwise, no unusual features of secondary structure or sequence are present. CARNA 5 (D) contains a number of possible initiation and termination codons for protein synthesis. Study of CARNA 5 isolated from other strains of cucumber mosaic virus suggests that sequence variation of the molecule from one strain to another is very limited.     

Complete genome sequence of a new begomovirus associated with yellow mosaic disease of Hemidesmus indicus in India

The complete DNA A genome of a virus isolate associated with yellow mosaic disease of a medicinal plant, Hemidesmus indicus, from India was cloned and sequenced. The length of DNA A was 2825 nucleotides, 35 nucleotides longer than the unit genome of monopartite begomoviruses. Comparison of the nucleotide sequence of DNA A of the virus isolate with those of other begomoviruses showed maximum sequence identity of 69 % to DNA A of ageratum yellow vein China virus (AYVCNV; AJ558120) and 68 % with tomato yellow leaf curl virus- LBa4 (TYLCV; EF185318), and it formed a distinct clade in phylogenetic analysis. The genome organization of the present virus isolate was found to be similar to that of Old World monopartite begomoviruses. The genome was considered to be monopartite, because association of DNA B and β satellite DNA components was not detected. Based on its sequence identity (<70 %) to all other begomoviruses known to date and ICTV (International Committee on Taxonomy of Viruses) species demarcating criteria (<89 % identity), it is considered a member of a novel begomovirus species, and the tentative name “Hemidesmus yellow mosaic virus” (HeYMV) is proposed.     

Complete sequence of the Pepino mosaic virus RNA genome

We have determined the complete nucleotide sequence (Accession No. AF484251) of the Pepino mosaic virus (PepMV) RNA genome. PepMV is the etiological agent of a new disease which affects tomato crops in Europe and North America. The PepMV genome consists of one single stranded positive sense RNA 6410 nt long that contains five open reading frames (ORFs). ORF 1 is the putative RNA dependent RNA polymerase (RdRp), as it has the characteristic methyltransferase, NTP-binding and polymerase motifs. ORF 2 to 4 form the PepMV triple gene block. ORF 5 codes for the capsid protein. Two short untranslated regions flank the coding regions and there is a poly(A) tail at the 3'end of the genomic RNA. Thus, the genome organization of PepMV is that of a typical member of the genus Potexvirus. The nucleotide sequence obtained shares an overall 99% identity with the genomic RNA of a PepMV isolate from UK which has been partially sequenced. Protein coded by ORF4 is the least conserved between both isolates (95% amino acid identity), whereas proteins coded by ORF3 and ORF5 are identical.     

Nucleotide sequence of a radiation leukemia virus genome

The complete nucleotide sequence of an infectious molecular clone of a radiation murine leukemia proviral DNA RadLV/VL3(T+L+) has been determined. The sequence of the RNA genome is 8318 nucleotides long and contains three large open reading frames encoding the gag, pol, and env gene products. With the exception of a xenotropiclike R peptide and the LTR which bears structural similarities to a xenotropic LTR, displaying typical enhancerlike sequences, the remaining sequences are strikingly similar to the endogenous, ecotropic Akv murine leukemia virus. Therefore, it could be postulated that the leukemogenic properties of RadLV/VL3(T+L+) were generated by a recombination event between a xenotropic virus and an Akv-like ecotropic virus.     

A tymovirus from Calopogonium mucunoides in Malaysia is not clitoria yellow vein tymovirus

Summary. A tymovirus isolated from Malaysian crops of Calopogonium mucunoides has been shown to have virions that are serologically indistinguishable from those of clitoria yellow vein tymovirus. We have sequenced the virion protein (VP) gene of the virus and have found that although it is a member of the cluster that includes CYVV, it is the most distinct member of that cluster (< 62% sequence identity with all the others), and is clearly a separate species, which we propose should be named calopogonium yellow vein virus. Most of the serological specificity of the virions of tymoviruses seems to reside in the C-terminal hexapeptide of the virion protein. Received December 12, 1996 Accepted March 7, 1997     

The complete genome sequence and genome structure of frangipani mosaic virus

In this study, the complete sequence of the genomic RNA of frangipani mosaic virus (FrMV) has been determined and compared to those of other known tobamoviruses. The complete genome sequence of FrMV consisted of 6,643 nucleotides. The FrMV genomic RNA encoded four open reading frames (ORFs), for proteins of M(r) 128 kDa (1,147 aa), 186 kDa (1,651 aa), 30 kDa (257 aa) and 18 kDa (175 aa) from the 5′ to the 3′ end. Overall similarities for the four ORFs of FrMV-P ranged from 26.8 to 53.0% at the amino acid level when compared to those of 24 other tobamoviruses. Phylogenetic analysis of the FrMV replicase (186 kDa) and MP revealed that FrMV is closely related to SHMV and CMMoV, while the FrMV replicase (128 kDa) is more closely related to cucurbit-infecting and malvaceous-infecting tobamoviruses, and the FrMV CP is closely related to that of CMMoV and solanaceous-infecting tobamoviruses.     

Nucleotide sequence of a Singapore isolate of zucchini yellow mosaic virus coat protein gene revealed an altered DAG motif

A cDNA clone of zucchini yellow mosaic virus (ZYMV) RNA was mapped to the 3 terminal region. The nucleotide sequence revealed a single open reading frame of 1035 nucleotides followed by a 3 noncoding region of 215 nucleotides. The putative protease cleavage site for the release of coat protein (CP) was deduced to be between Glu-Ser (at amino acid position 66–67), which would result in a protein of 279 amino acids. This non-aphid-transmissible Singapore isolate of ZYMV showed a change of DAG to GAG triplet near the N-terminal of the CP. The CP gene was expressed as a protein fused to the -galactosidase inEscherichia coli and as an unfused protein inSaccharomyces cerevisiae.The nucleotide sequence data reported in this paper have been submitted to the EMBL nucleotide sequence database and have been assigned the accession number X62662.     

Nucleotide sequence of pea seed-borne mosaic potyvirus coat protein gene

cDNA of pea seed-borne mosaic potyvirus (PSbMV) RNA was synthesized and cloned in E. coli. Four overlapping clones that cover the complete PSbMV genome, except the extreme 5 terminus, were identified by restriction enzyme mapping, hybridization analysis, and partial sequencing. Overlapping cDNA clones covering 1386 nucleotides of the 3 terminus were sequenced. The nucleotide sequence contains one open reading frame (ORF), followed by an untranslated region of 163 nucleotides and a poly(A)-tract. The deduced amino acid sequence was found to include the C-terminus of the predicted RNA-dependent RNA polymerase and the coat protein. A glutamine-alanine dipeptide was identified as a putative 49-kD proteinase cleavage site at the N-terminus of the coat protein.