Molecular evidence that zucchini yellow fleck virus is a distinct and variable potyvirus related to papaya ringspot virus and Moroccan watermelon mosaic virus

Summary. Zucchini yellow fleck virus (ZYFV, genus Potyvirus) infects cultivated or wild cucurbits in the Mediterranean basin and occasionally causes severe damage in crops. Biological and serological data tend to indicate that ZYFV is related to other cucurbit-infecting potyviruses, mainly papaya ringspot virus (PRSV) and Moroccan watermelon mosaic virus (MWMV). In order to establish unambiguously the taxonomic status of ZYFV, the sequence of the 3′ part of the genome – encompassing the CP coding region – of two ZYFV strains originating from Italy and France was obtained and compared with other potyviruses. The results obtained indicate that ZYFV belongs to a distinct potyvirus species, related to but different from PRSV and MWMV.     

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.     

Nucleotide sequence of the coat protein coding region of the potyvirus tobacco vein-banding mosaic virus

Summary The sequence of the 3 1184 nucleotides of tobacco vein-banding mosaic virus (TVBMV) genome has been determined. It contains a single open reading frame which encompasses the whole of the coat protein of TVBMV. The sequence of the first 20 amino acids at the N-terminal region of the coat protein has also been determined chemically to be GDDQTVDAGKNVQSNQKQRN. The sequence matches the translation product of the open reading frame starting with amino acid-271; a glycine residue. Thus the coat protein of TVBMV has a calculated M_r of 30 210. The 3 non-coding region of TVBMV is 185 nucleotides in length. Sequence alignment of the coat proteins or the 3 non-coding regions from TVBMV and other reported potyviruses indicated that TVBMV is a separate species of the potyvirus genus.     

Complete genome sequence of keunjorong mosaic virus, a potyvirus from Cynanchum wilfordii

We have determined the complete genome sequence of keunjorong mosaic virus (KjMV). The KjMV genome is composed of 9,611 nucleotides, excluding the 3′-terminal poly(A) tail. It contains two open reading frames (ORFs), with the large one encoding a polyprotein of 3,070 amino acids and the small overlapping ORF encoding a PIPO protein of 81 amino acids. The KjMV genome shared the highest nucleotide sequence identity (57.5  %) with pepper mottle virus and freesia mosaic virus, two members of the genus Potyvirus. Based on the phylogenetic relatedness to known potyviruses, KjMV appears to be a member of a new species in the genus Potyvirus.     

Nucleotide sequence of the capsid protein gene of papaya leaf-distortion mosaic potyvirus

Summary The DNA complementary to the 3-terminal 1 404 nucleotides [excluding the poly(A) tail] of papaya leaf-distortion mosaic potyvirus (PLDMV) RNA was cloned and sequenced. The sequence starts within a long open reading frame (ORF) of 1 195 nucleotides and is followed by a 3 non-coding region of 209 nucleotides. Capsid protein (CP) is encoded at the 3 terminus of the ORF. The CP contains 293 residues and has a M_r of 33 277. The CP of PLDMV exhibits 49 to 59% sequence similarity at the amino acid level to the CPs of papaya ringspot potyvirus (PRSV) and other potyviruses. This result is consistent with the absence of a serological relationship between PLDMV and PRSV or other potyviruses. The results support the assignment of PLDMV as a distinct member of the genusPotyvirus.Sequence data from this article has been deposited with the EMBL/GenBank/DDBJ databases under accession no. D50082.     

Genome sequence of vanilla distortion mosaic virus infecting Coriandrum sativum

The 9573-nucleotide genome of a potyvirus was sequenced from a Coriandrum sativum plant from India with viral symptoms. On analysis, this virus was shown to have greater than 85 % nucleotide sequence identity to vanilla distortion mosaic virus (VDMV). Analysis of the putative coat protein sequence confirmed that this virus was in fact VDMV, with greater than 91 % amino acid sequence identity. The genome appears to encode a 3083-amino-acid polyprotein potentially cleaved into the 10 mature proteins expected in potyviruses. Phylogenetic analysis confirmed that VDMV is a distinct but ungrouped member of the genus Potyvirus.     

The genomic sequence and biological properties of Pennisetum mosaic virus, a novel monocot-infecting potyvirus

The complete nucleotide sequences of two isolates of Pennisetum mosaic virus (PenMV) were determined. The viral genome comprised 9,611 nucleotides (nt) excluding the 3′-terminal poly(A) sequence, with the capacity of encoding a single polyprotein of 3,065 amino acids. The large open reading frame is flanked by a 172-nt 5′-untranslated region (UTR) and a 244-nt 3′-UTR. Sequence comparisons and phylogenetic analyses of the complete genome and polyproteins suggest that PenMV is closely related to other monocot potyviruses such as Maize dwarf mosaic virus, Sorghum mosaic virus and Sugarcane mosaic virus (SCMV), and thus represents a distinct potyvirus within the SCMV subgroup. The host range of PenMV is limited to Gramineae, and the virus naturally infects maize, sorghum and some wild grasses, causing mosaic symptoms on the leaves. This virus could be transmitted by both mechanical inoculation and by at least four species of aphids.     

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.     

Zantedeschia mosaic virus causing leaf mosaic symptom in calla lily is a new potyvirus

Anovel virus, Zantedeschia mosaic virus (ZaMV-KR), causing mosaic and malformation symptoms was isolated from calla lily ( Zantedeschia spp.) in Korea and its biological and molecular properties were characterized. The virus was distinct from Dasheen mosaic virus, an Araceae-infecting potyvirus, by serological and sequence analyses. Multiple alignments of the CP amino acid sequence between the virus and other potyviruses showed 51.8 to 62.1% identity. Phylogenetic analyses of the CP revealed that the virus could be clustered with Plum pox virus and Turnip mosaic virus. Sequence comparison of the CP gene between the virus and three other ZaMV isolates from Taiwan showed over 93.9% identity, and most of amino acids changes occurred in the N-terminal region. Sequence comparison of 3' NTR revealed homology levels of 27.0 to 47.9% between the virus and other potyviruses. Our results support ZaMV as a distinct species of the genus Potyvirus.     

Nucleotide sequence of the coat protein cistron and the 3' noncoding region of cucumber green mottle mosaic virus (watermelon strain) RNA

Double-stranded cDNA copies of cucumber green mottle mosaic virus (watermelon strain, CGMMV-W) RNA polyadenylated in vitro were cloned into the pBR322 at the PstI site. The sequence of 1071 nucleotides from the Tend of the genomic RNA was determined using two recombinant plasmids and the genomic RNA. The coat protein cistron was located in residues 176-661 from the 3' end. The coat protein was composed of 160 amino acid residues with the molecular weight of 17,261. The 3' noncoding region of the CGMMVW genome was 175 nucleotides long and highly homologous to that of the common strain of TMV. The assembly origin of reconstitution is positioned within the coat protein cistron as predicted previously. In the 5' flanking region of the coat protein cistron a long open frame, probably of 30K protein, was found. The predicted 30K and the coat protein cistron would overlap each other as is the case of the cowpea strain of TMV.     

Serological and coat protein sequence studies suggest that necrosis disease on sunflower in India is caused by a strain of Tobacco streak ilarvirus

Summary.  Serological and coat protein sequence studies were conducted to identify an ilarvirus associated with necrosis disease on sunflower in India. In electroblot immunoassay, sunflower ilarvirus reacted strongly only with antiserum to Tobacco streak virus (TSV). The coat protein gene of sunflower ilarvirus was cloned and sequenced. The sequence analyses also showed that the CP gene was most closely related to TSV, the member of subgroup I of Ilarvirus. The sunflower ilarvirus CP shared 90% amino acid sequence identity with TSV. On the basis of serological relatedness and sequence identity, it is proposed that the sunflower ilarvirus from India should be considered a strain of TSV belonging to subgroup I and designated as TSV-SF. This is the first report of the molecular characterization of TSV on sunflower from the Indian subcontinent. Received August 9, 2001 Accepted October 11, 2001     

Nucleotide sequence and translation of satellite tobacco mosaic virus RNA

Satellite tobacco mosaic virus (STMV) is a plant virus with a 17-nm icosahedral particle encapsidating a 0.3 X 10(6) Mr ssRNA genome that depends on tobamoviruses for its replication. The complete nucleotide sequence of STMV RNA deduced in the experiments described here was 1059 nucleotides in length. The efficiency of labeling viral RNA with [gamma-32P]ATP using T4 polynucleotide kinase was not affected by treatment with tobacco acid pyrophosphatase and/or bacterial alkaline phosphatase, indicating that the majority of the 5' termini of encapsidated STMV RNAs were not phosphorylated. The 240 3'-terminal nucleotides of STMV RNA and either tobacco mosaic virus (TMV) U1 RNA or TMV U2/U5 RNA had greater than 65% overall sequence similarity, with two nearly identical regions of 40 and 50 bases, respectively. There were no other regions of sequence relatedness to TMV RNA. The 19 5'-terminal nucleotides of STMV RNA had greater than 65% sequence similarity with the 16 5'-terminal nucleotides of brome mosaic virus (RNA 3 and 50% sequence similarity with the 12 5'-terminal nucleotides of the Q strain of cucumber mosaic virus RNA 3. The first open reading frame (ORF) beginning at base 53 encoded a 6800 Mr protein that corresponded in size to a major in vitro translation product directed by STMV RNA. A second ORF, beginning at nucleotide 163, had the capacity to code for a protein that corresponded in size (17,500 Mr) to the other major in vitro translation product. The first 12 codons of this ORF corresponded to the sequence of the N-terminal amino acids of the capsid protein. Western-blot analysis of the in vitro translation products revealed that the 17,500 Mr protein had the same electrophoretic mobility as the authentic capsid protein; it was also antigenically related to the capsid protein, but the 6800 Mr protein was not. Time course analysis of in vitro translation demonstrated that the 6800 Mr protein was synthesized at the same time as the capsid protein and did not arise by the proteolytic cleavage of a larger precursor polypeptide. These results suggest that the genome of STMV functioned as a polycistronic messenger RNA. It has not been determined if the 6800 Mr protein is synthesized in vivo. STMV RNA had untranslated regions of 52 and 418 nucleotides at its 5' and 3' termini, respectively.(ABSTRACT TRUNCATED AT 400 WORDS)     

Nucleotide sequence and infectious cDNA clone of the L1 isolate of Pea seed-borne mosaic potyvirus

Summary.   The complete nucleotide sequence of Pea seed-borne mosaic potyvirus isolate L1 has been determined from cloned virus cDNA. The PSbMV L1 genome is 9895 nucleotides in length excluding the poly(A) tail. Computer analysis of the sequence revealed a single long open reading frame (ORF) of 9594 nucleotides. The ORF potentially encodes a polyprotein of 3198 amino acids with a deduced Mr of 363537. Nine putative proteolytic cleavage sites were identified by analogy to consensus sequences and genome arrangement in other potyviruses. Two full-length cDNA clones, p35S-L1-4 and p35S-L1-5, were assembled under control of an enhanced 35S promoter and nopaline synthase terminator. Clone p35S-L1-4 was constructed with four introns and p35S-L1-5 with five introns inserted in the cDNA. Clone p35S-L1-4 was unstable in Escherichia coli often resulting in amplification of plasmids with deletions. Clone p35S-L1-5 was stable and apparently less toxic to Escherichia coli resulting in larger bacterial colonies and higher plasmid yield. Both clones were infectious upon mechanical inoculation of plasmid DNA on susceptible pea cultivars Fjord, Scout, and Brutus. Eight pea genotypes resistant to L1 virus were also resistant to the cDNA derived L1 virus. Both native PSbMV L1 and the cDNA derived virus infected Chenopodium quinoa systemically giving rise to characteristic necrotic lesions on uninoculated leaves. Received Jnuary 24, 2000 Accepted August 1, 2000     

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.     

Complete nucleotide sequence of the geonomic RNA of a mild strain of Japanese yam mosaic potyvirus

Summary.  We determined the complete nucleotide sequence of a mild strain of Japanese yam mosaic potyvirus (JYMV-M) and compared it with the published sequence of severe strain of JYMV (JYMV-J1). The genomic RNA of JYMV-M is 9,760 nucleotides (nts) in length, excluding the poly (A) tail, and encodes a polyprotein of 3,132 amino acids. Among nine potential cleavage sites, only the P1 and NIa recognition sites (between 6K1 and CI) had different sequences from those of JYMV-J1. The data confirm the strain status of these two viruses with 91.1% sequence identity for the polyprotein and ∼94–97% identities for HC, CI, NIa, NIb and CP. The most divergent products P1 and P3 had 62% and 90% sequence identities respectively. Accepted September 27, 1999     

Nucleotide sequence of a resistance breaking mutant of southern bean mosaic virus

Summary.  SBMV-S is a resistance-breaking mutant of an Arkansas isolate of the bean strain of southern bean mosaic virus (SBMV-B^ARK) that is able to move systemically in Phaseolus vulgaris cvs. Pinto and Great Northern, whereas the wild-type SBMV-B^ARK causes local necrotic lesions and is restricted to the inoculated leaves of these hosts. Sequence analysis of the 4136 nucleotide genomes of SBMV-B^ARK and SBMV-S revealed seven nucleotide differences, but only four deduced amino acid changes. A single amino acid change occurred in the C-terminal region of the putative RNA-dependent RNA polymerase and three differences were identified in the N-terminal portion of the virus coat protein. SBMV-B^ARK and SBMV-S were compared with other sobemoviruses and were found to contain a high level of nucleotide sequence identity (91.3%) to SBMV-B. Unlike SBMV-B however, SBMV-B^ARK and SBMV-S contained four putative overlapping open reading frames, making them more similar in genome organization to the cowpea strain, SBMV-C. The possibility exists that mutations or even errors, that resulted in mis-identification of open reading frames, occurred in previously published information on nucleotide sequence and genomic organization for SBMV-B. Received November 23, 1997 Accepted June 16, 1998     

Complete nucleotide sequence of the genomic RNA of a Japanese yam mosaic virus, a new potyvirus in Japan

Summary.  We determined the complete nucleotide sequence of a potyvirus purified from a Japanese yam plant. The genomic RNA of this virus is 9 757 nucleotides (nts) in length, excluding the 3′-terminal poly(A) tail. It contains a single open reading frame (ORF) encoding a polyprotein of 3130 amino acids (aa) with a calculated Mr of 356,793. The genomic organization of this potyvirus is similar to that of other members of the genus Potyvirus and nine potential cleavage sites for the viral proteinase were found by comparison of its sequence with those available for other potyviruses. The nucleotide sequence and genome characteristics show that this isolate is a new potyvirus species. Its polyprotein differs substantially from Yam mosaic virus (YMV) (50% amino acid sequence identity) and fourteen other potyvirus species examined (44–59% identity). Although this potyvirus has been classified as YMV, our results suggest that the potyvirus infectious to the Japanese yam plant in Japan is distinct from YMV. Therefore, we propose that the Japanese yam potyvirus should be designated as Japanese yam mosaic virus (JYMV). September 14, 1998 Received August 3, 1998     

Vanilla mosaic virus isolates from French Polynesia and the Cook Islands are Dasheen mosaic virus strains that exclusively infect vanilla

Summary. Sequence was determined for the coat protein (CP) gene and 3′ non-translated region (3′NTR) of two vanilla mosaic virus (VanMV) isolates from Vanilla tahitensis, respectively from the Cook Islands (VanMV-CI) and French Polynesia (VanMV-FP). Both viruses displayed distinctive features in the N-terminal region of their CPs; for VanMV-CI, a 16-amino-acid deletion including the aphid transmission-related DAG motif, and for VanMV-FP, a stretch of GTN repeats that putatively belongs to the class of natively unfolded proteins. VanMV-FP CP also has a novel DVG motif in place of the DAG motif, and an uncommon Q//V protease cleavage site. The sequences were compared to a range of Dasheen mosaic virus (DsMV) strains and to potyviruses infecting orchids. Identity was low to DsMV strains across the entire CP coding region and across the 3′NTR, but high across the CP core and the CI-6K2-NIa region. In accordance with current ICTV criteria for species demarcation within the family Potyviridae, VanMV-CI and VanMV-FP are strains of DsMV that exclusively infect vanilla.