A phylogenetic reexamination of Cucumber mosaic virus isolates (original) (raw)
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Nucleotide Sequence and Evolutionary Relationships of Cucumber Mosaic Virus (CMV) Strains: CMV RNA 1
Journal of General Virology, 1989
The nucleotide sequence of RNA 1 of the Fny strain (Subgroup I) of cucumber mosaic virus (CMV) was determined and compared at both the nucleic acid and protein levels with the corresponding sequence of RNA 1 of the Q strain (Subgroup II) of CMV. Fny-CMV RNA 1 consisted of 3357 nucleotides and contained a single long open reading frame (ORF) of 2979 nucleotides, whereas Q-CMV RNA 1 consists of 3389 nucleotides and contains a single ORF of 2973 nucleotides. The levels of sequence homology between the two RNAs were 76~ at the nucleotide level and 85~o at the protein level. These homologies were distributed widely over the molecules, with 45 of the non-conservative differences in amino acid sequence located between amino acids 503 and 705, and another 15 ~ of the differences located between amino acids 224 and 298. While the C-terminal 141 amino acids contain more basic than acidic amino acids, the region of greatest amino acid sequence heterogeneity, amino acids 503 to 600, contained a preponderance of acidic amino acids in the putative translation products of RNAs 1 of both Q-CMV and Fny-CMV. The last 180 nucleotides of the 3'-terminal non-coding region of Fny-CMV RNAs 1 and 2 were 96~ homologous, whereas the sequence homology between Fny-CMV RNA 1 and Q-CMV RNA 1 was 64~ in this region. Furthermore, the tRNA-like secondary structures formed by the 3'-terminal non-coding regions of Fny-CMV RNAs 1 and 2 were virtually identical. By contrast, there was only 84~ sequence homology between the 5"-terminal non-coding regions of these two RNAs and 81~ sequence homology between the 5'-terminal non-coding regions of Q-CMV RNA 1 and Fny-CMV RNA 1. The non-equivalent divergence in the non-coding regions of these RNAs, as well as possible functions for the translation product of RNA 1, are discussed.
The Plant Pathology Journal, 2012
Molecular characterization of Cucumber mosaic virus (CMV) was done by using samples from tomato and cucurbitaceous plants collected from different locations in the northwest region of Iran. After screening by enzyme-linked immunosorbent assay, 91 CMV-infected samples were identified. Biological properties of eight representative isolates were compared with each other revealing two distinct phenotypes on squash and tomato plants. Phylogenetic analyses based on nucleotide sequences of the coat protein (CP), movement protein (MP) and 2b of the new isolates, together with that of previously reported isolates, led to the placement of the Iranian isolates in subgroups IA and IB according to CP and MP genes, but in subgroup IA according to the 2b gene. These data suggest that reassortment may have been a major event in the evolution of CMV in Iran, and that the Iranian isolates are derived from a common recent ancestor that had passed through a bottleneck event.
Nucleotide sequence and evolutionary relationships of cucumber mosaic virus (CMV) strains: CMV RNA 3
Journal of General Virology, 1990
The nucleotide sequence of RNA 2 of the Fny strain (Subgroup I) of cucumber mosaic virus (CMV) was determined and compared at both the nucleic acid and protein level with the previously determined corresponding sequence of RNA 2 of the Q strain (Subgroup 2) of CMV. Fny-CMV RNA II 2 consisted of 3050 nucleotides and contained a single open reading frame (ORF) of 2571 nucleotides, whereas Q-CMV RNA 2 consists of 3035 nucleotides and contains a single ORF of 2517 nucleotides. At the nucleotide level, there was 71 ~ sequence homology between the two RNAs, while at the protein level sequence homology was 73 ~. Protein homology was greater (89 ~) in the central third than in either the N-terminal (64 ~) or the C-terminal (56 ~o) thirds. The secondary structures of the 3' end of the RNAs were very similar, even though the nucleotide sequence homology between the Y-terminal 180 nucleotides was only 62 ~. By contrast, there was 80~ sequence homology between the Y-terminal 86 residue, non-translated regions of the two RNAs. The evolutionary relationships and the divergence and retention of specific sequences among the two CMV strains and other plant viruses are discussed. 0000-8270 © 1988 SGM T. M. RIZZO AND P. PALUKAITIS
Journal of General Virology, 1989
The complete nucleotide sequence (2217 residues) of RNA 3 of cucumber mosaic virus strain O (CMV-O) was determined. Two open reading frames were identified, encoding a 3A protein (279 amino acid residues) in the Y-proximal region and a coat protein (218 amino acid residues). The amino acid sequence of the coat protein C terminus was determined directly from purified protein, and confirmed the presence of the coat protein open reading frame in CMV-O RNA 3. Comparison of nucleotide sequences and amino acid sequences of CMV strains O, Q, D and Y indicated the close relationship between these strains. A tRNA-like structure could be adopted by the 3' non-coding region, and this resembled a similar structure in CMV-Q in spite of nucleotide substitutions or deletions. Cucumber mosaic virus (CMV), a multicomponent virus of the cucumovirus group (Kaper & Waterworth, 1981), has a single-stranded plus-sense RNA genome consisting of three RNA species which are designated RNA 1, 2 and 3 in order of decreasing Mr. In addition, there is a fourth RNA, RNA 4, which is subgenomic to RNA 3 and is reported to serve as a monocistronic messenger for in vitro synthesis of the coat protein (Schwinghamer & Symons, 1977). RNA 3 encodes two in vitro translation products, a 3A protein and a coat protein. By comparison with the function of tobacco mosaic virus 30K protein, the 3A protein is deduced to be responsible for cell-to-cell movement (Meshi et al., 1987). Some strains have a small virus-dependent satellite RNA, RNA 5, which has been demonstrated to alter the symptoms of disease (Kaper & Waterworth, 1977). CMV is one of the most widespread plant viruses; up to now more than 60 strains have been reported. These strains have been studied and characterized according to their symptoms in indicator hosts, their serology and particle morphology (Kaper & Waterworth, 198 l). However, there is only one strain (CMV-Q) for which the complete sequences of the four RNA species have been determined (Gould & Symons, 1982; Rezaian et al., 1984, 1985). Recently, the sequence of CMV-Q RNA 3 has been revised by Davies & Symons (1988). Although a comparative study of nucleotide sequence has been reported for the satellite RNA (Richards et al., 1978; Kaper et al., 1988), such studies on genomic RNAs have not yet been reported. Hidaka et al. (1985) determined a 106 nucleotide sequence at the Y-terminal region of CMV-Y RNA 4 using a direct RNA sequencing method. Recently, Cuozzo et al. (1988) reported an almost complete sequence for CMV-D RNA 4. It will be of interest to discover whether or not differences of nucleotide sequences relate to each strain's characteristics, such as symptoms of disease or host specificity. However, the partial sequences of the CMV-Y and CMV-D subgenomic RNAs are not sufficient for comparison. Thus, determination of the complete sequences of other CMV RNA genomes in addition to strain Q has been awaited. We present here the complete nucleotide sequence of RNA 3 of CMV-O, which was isolated
Plant Protection Science, 2015
Using double-antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA), Cucumber mosaic virus (CMV) was detected in 31 out of 132 symptomatic leaf samples collected from different hosts of Urmia province of Iran, during 2011-2012. In biological assays, five different host isolates caused severe mosaic in Nicotiana species and Capsicum annum without significant difference in severity. Based on phylogenetic analysis of coat protein nucleotide and deduced amino acid sequence, two isolates were clustered into subgroup IA, while other three isolates were grouped into IB subgroup of CMV. All Urmian isolates shared a common MspI, and no EcoRI and BsuRI restriction sites. In contrast to S-IA isolates, the second MspI site was found at 473-476 position of only S-IB isolates, which could be used to differentiate two S-IA and S-IB subgroups. Here, we report the first case of Abutilon theophrasti infection, as a new reservoir weed host for CMV in the world.
Journal of Crop Protection, 2019
Cucumber mosaic virus (CMV; genus Cucumovirus, family: Bromoviridae) has the widest host range of any known plant viruses. Seven virus isolates, originated from different ornamental plant species and greenhouses, were biologically purified, mechanically inoculated onto test plants and their serological differences were assayed based on reactivity with 11 CMV-specific monoclonal antibodies. Following total RNA extraction, coat protein (CP) coding region of CMV isolates was amplified. Based on biological, serological and phylogenetic analysis, only one isolate belonged to CMV subgroup II and other six isolates were equally distributed among the two IA and IB subgroups. Aphid transmission assay showed that no significant difference was observed between transmission efficiency of CMV subgroups IA, IB and II members by Aphis gossypii. The genetic variation and evolution of CMV in Iran was studied by sequence analysis of the CP gene and comparison with equivalent sequences of isolates fro...
Virology, 1988
RNAs from 13 strains of cucumber mosaic virus (CMV) were divided into two groups on the basis of their ability to hybridize to cDNA of either Fny-CMV RNA or WL-CMV RNA. The extent of the cross-hybridization within one of these groups was analyzed by an RNA protection assay. A cDNA clone of RNA 3 of the Fny strain of CMV was placed in a transcription vector between bacterial promoters T3 and T7. Labeled, minus-sense RNA transcripts prepared from all or part of the cDNA to RNA 3 of Fny-CMV were annealed to the genomic RNA of each of a number of cucumoviruses and digested with RNases. The patterns of RNA fragments protected from digestion were specific for each CMV strain and revealed the extent and location of heterogeneity among the viruses as well as within the Fny-CMV natural population. This approach will allow the differences in host range and disease processes to be correlated with variations in genomic RNAs.
Virus Research, 1994
The complete nucleotide sequence (2209 nucleotides) of the RNA 3 of the cucumber mosaic virus strain Trk7 was determined. Trk7-CMV possesses two open reading frames which encode the 3a protein (279 amino acids) and the coat protein (218 amino acids). Sequence analysis proved the earlier biological and serological classification of the RNA 3 molecule of Trk7-CMV in subgroup II. A high degree of homology was found in the strains Q and Kin of CMV, while the average similarity between the two different subgroups is much lower.
Genealogy of Cucumber mosaic virus Isolated from Ornamental Species
American Journal of Plant Sciences, 2013
Cucumber mosaic virus (CMV) has the broadest host range, infecting more than 1300 species in more than 500 genera from over 100 botanical families. In ornamental plants, CMV can cause mosaic and distortion of leaves, stunting, color break, and malformation of flowers. CMV coat protein (CP) sequences obtained from seven ornamental plants and other homologous sequences available in GenBank were compared, and phylogenetic relationships were established. Total RNA from virus-infected ornamental species were extracted, submitted to RT-PCR with specific primers, and amplicons obtained were sequenced. A nucleotide substitution model and phylogenetic analyses were carried out using the PAUP program. The seven sequences of CMV CP obtained showed similar identity percentages and close relationships with subgroup I isolates from other countries and hosts. CMV isolates from different regions of São Paulo state, Brazil (Salvia splendens, Catharanthus roseus, Nematanthus nervosus (=Hypocyrta nervosa), Impatiens walleriana, Eucharis grandiflora and Commelina sp.) formed a monophyletic group, indicating a possible common origin. It was found that when lily sequences of CMV only from different geographic regions were compared, Brazilian isolates shared the same common ancestor with those from Poland and Taiwan. Furthermore, this monophyletic group presented a quite basal position.