Complete Genome Sequence and Genome Analysis of Eggplant mottled dwarf virus‐Iranian Isolate

The full‐length nucleotide sequence of the Iranian isolate of Eggplant mottled dwarf virus (EMDV), a phytorhabdovirus, was determined using the random polymerase chain reaction method (rPCR) followed by PCR with specific primers to fill in the gaps. The negative‐sense RNA genome of the Iranian isolate of EMDV contains 13154 nucleotides and seven open‐reading frames (ORFs) in the order 3′‐leader‐N‐X‐P‐Y‐M‐G‐L‐trailer‐5′. These ORFs encode the nucleocapsid, X protein (of unknown function), phosphoprotein, Y protein (putative movement protein), matrix protein, glycoprotein and RNA‐dependent RNA polymerase, respectively. EMDV has a 199 nt 3′ leader RNA and a 151 nt 5′ trailer, and the ORFs are separated by conserved intergenic sequences. Phylogenetic analyses indicate that EMDV is most closely related to Potato yellow dwarf virus, which has a distinctly different geographical distribution.     

Molecular characterization of a new badnavirus associated with streak symptoms on enset (Ensete ventricosum,Musaceae)

Electron microscopy of leaf samples displaying streak symptoms from enset (Ensete ventricosum), a banana‐like plant widely cultivated in Ethiopia, showed the presence of bacilliform shaped virions as known for badnaviruses. DNA extracts subjected to rolling circle amplification (RCA), polymerase chain reaction (PCR) and cloning and sequence analysis revealed that the virus has a circular double‐stranded DNA genome of 7,163 nucleotides encoding predicted proteins of 21.5 kDa, 14.5 kDa and 202.5 kDa, a genome organization known for badnaviruses. The virus is phylogenetically most closely related to Sugarcane bacilliform Guadeloupe D virus with a nucleotide sequence identity of 77.2% at the conserved RT/RNase‐H region and 73.6% for the whole genome. Following the current species demarcation criteria, the virus should be considered as an isolate of a new species in the genus Badnavirus for which the name Enset leaf streak virus (ELSV) is suggested. Leaf samples from enset and banana were screened using virus‐specific primers, and ELSV was detected in six of 40 enset but not found in any of 61 banana samples. On the other hand, Banana streak OL virus (BSOLV) was detected from the majority (60%) of symptomatic banana samples but not from enset samples. This paper reports the first full‐genome sequence of a putative new badnavirus species infecting plants in the genus Ensete. In addition, this is the first report of the occurrence of BSOLV in Ethiopia.     

Analysis of the Complete Nucleotide Sequence of the Polymerase Gene of Barley Yellow Striate Mosaic Virus– Iranian Isolate

The complete nucleotide sequence of an Iranian isolate of Barley yellow striate mosaic virus (BYSMV) L gene comprising 6171 nucleotides was determined using the random polymerase chain reaction followed by filling of gaps by the use of specific primers. The deduced L protein sequence of BYSMV showed similarities with the L proteins of other plant rhabdoviruses and contained polymerase module motifs characteristic of RNA‐dependent RNA polymerases of negative‐strand RNA viruses. Pairwise and multiple alignments and phylogenetic analysis of BYSMV L protein revealed that it was more closely related to cytorhabdoviruses. These results revealed that, on the basis of polymerase gene, the Iranian isolate of BYSMV and Northern cereal mosaic virus (NCMV) appeared to be the most closely related plant rhabdoviruses sequenced to date. Interestingly, the amino acid sequence identity of BYSMV/NCMV (61.3%), shared more than twice the amino acid sequence identity compared with the next two most similar cytorabdoviruses, Lettuce necrotic yellows virus (28.8%) and Lettuce yellow mottle virus (28.2%). In this paper, we discuss the similarities and differences of BYSMV with other rhabdoviruses which support the classification of BYSMV as a distinct Cytorhabdovirus. This is the first report of BYSMV genome sequences.     

The complete sequence of a Singapore isolate of odontoglossum ringspot virus and comparison with other tobamoviruses

The complete sequence of a Singapore isolate of odontoglossum ringspot virus (ORSV-S1) comprises 6609 nucleotides (nt) and four open reading frames (ORFs 1 to 4). The 126/183-kDa RNA-dependent RNA polymerase (RdRp), 33-kDa movement protein (MP) and 18-kDa coat protein (CP) cistrons are located at nt 63-3401/4901, 4807–5718, and 5721–6197 on the genome, respectively. The 5′ UTR contains three copies of an 8-base direct repeat and (CAA)_n motifs. Characteristic tRNA-like structure and three consecutive homologous regions were present in the 3′ UTR. The genomic RNA and MP of ORSV-S1 are one of the longest among all members of the TOV group. Phylogenetic analysis of all four genes indicates evolutionary divergence, but within each gene there are some degrees of evolutionary convergence. The conserved amino acid sequences in the MP can be used for the classification of tobamoviruses.     

Isolation and characterization of a single‐stranded RNA virus that infects the marine planktonic diatom Chaetoceros sp. (SS08‐C03)

Diatoms are the major primary producers in the world's aquatic environment; hence, their dynamics are an important focus in current studies. Viruses, along with other physical, chemical, and biological factors, have recently been recognized as potential factors of diatom mortality. We isolated and characterized a new diatom virus (Csp03RNAV) that causes lysis of the marine planktonic diatom Chaetoceros sp. strain SS08‐C03 isolated from Hiroshima Bay, Japan. Here, we present the physiology, morphology, and genome characteristics of this virus. Csp03RNAV was isolated from surface waters of Yatsushiro Sea, Japan. Virions were icosahedral and 32 nm in diameter, and accumulated in the cytoplasm of the host cells. The latent period was estimated to be <48 h. Csp03RNAV harbors a single‐stranded RNA genome, which has 9417 bases encoding two open reading frames that code for putative replication‐related proteins and putative structural proteins, respectively. The monophyly of Csp03RNAV and the other known diatom‐infecting single‐stranded RNA viruses (genus Bacillarnavirus), Rhizosolenia setigera RNA virus, Chaetoceros socialis f. radians RNA virus, and Chaetoceros tenuissimus RNA virus was strongly supported by phylogenetic analysis based on the amino acid sequence of the RNA‐dependent RNA polymerase domain. On the basis of these results, Csp03RNAV is considered to be a new member of the genus Bacillarnavirus.     

Synergistic interactions of begomoviruses with Sweet potato chlorotic stunt virus (genus Crinivirus) in sweet potato (Ipomoea batatas L.)

Three hundred and ninety‐four sweet potato accessions from Latin America and East Africa were screened by polymerase chain reaction (PCR) for the presence of begomoviruses, and 46 were found to be positive. All were symptomless in sweet potato and generated leaf curling and/or chlorosis in Ipomoea setosa. The five most divergent isolates, based on complete genome sequences, were used to study interactions with Sweet potato chlorotic stunt virus (SPCSV), known to cause synergistic diseases with other viruses. Co‐infections led to increased titres of begomoviruses and decreased titres of SPCSV in all cases, although the extent of the changes varied notably between begomovirus isolates. Symptoms of leaf curling only developed temporarily in combination with isolate StV1 and coincided with the presence of the highest begomovirus concentrations in the plant. Small interfering RNA (siRNA) sequence analysis revealed that co‐infection of SPCSV with isolate StV1 led to relatively increased siRNA targeting of the central part of the SPCSV genome and a reduction in targeting of the genomic ends, but no changes to the targeting of StV1 relative to single infection of either virus. These changes were not observed in the interaction between SPCSV and the RNA virus Sweet potato feathery mottle virus (genus Potyvirus), implying specific effects of begomoviruses on RNA silencing of SPCSV in dually infected plants. Infection in RNase3‐expressing transgenic plants showed that this protein was sufficient to mediate this synergistic interaction with DNA viruses, similar to RNA viruses, but exposed distinct effects on RNA silencing when RNase3 was expressed from its native virus, or constitutively from a transgene, despite a similar pathogenic outcome.     

Characterisation of a novel Emaravirus identified in mosaic-diseased Eurasian aspen (Populus tremula)

Since Emaraviruses have been discovered in 2007 several new species were detected in a range of host plants. Five genome segments of a novel Emaravirus from mosaic-diseased Eurasian aspen (Populus tremula) have been completely determined. The monocistronic, segmented ssRNA genome of the virus shows a genome organisation typical for Emaraviruses encoding the viral RNA-dependent RNA polymerase (RdRP, 268.2 kDa) on RNA1 (7.1 kb), a glycoprotein precursor (GPP, 73.5 kDa) on RNA2 (2.3 kb), the viral nucleocapsid protein (N, 35.6 kDa) on RNA3 (1.6 kb), and a putative movement protein (MP, 41.0 kDa) on RNA4 (1.6 kb). The fifth identified genome segment (RNA5, 1.3 kb) encodes a protein of unknown function (P28, 28.1 kDa). We discovered that it is distantly related to proteins encoded by Emaraviruses, such as P4 of European mountain ash ringspot-associated virus. All proteins from this group contain a central hydrophobic region with a conserved secondary structure and a hydrophobic amino acid stretch, bordered by two highly conserved positions, thus clearly representing a new group of homologues of Emaraviruses. The virus identified in Eurasian aspen is closely associated with observed leaf symptoms, such as mottle, yellow blotching, variegation and chloroses along veins. All five viral RNAs were regularly detectable by RT-PCR in mosaic-diseased P. tremula in Norway, Finland and Sweden (Fennoscandia). Observed symptoms and testing of mosaic-diseased Eurasian aspen by virus-specific RT-PCR targeting RNA3 and RNA4 confirmed a wide geographic distribution of the virus in Fennoscandia. We could demonstrate that the mosaic-disease is graft-transmissible and confirmed that the virus is the causal agent by detection in symptomatic, graft-inoculated seedlings used as rootstocks as well as in the virus-infected scions used for graft-inoculation. Owing to these characteristics, the virus represents a novel species within the genus Emaravirus and was tentatively denominated aspen mosaic-associated virus.     

Molecular characterisation and relative incidence of bean‐ and soybean‐infecting begomoviruses in northwestern Argentina

Recent studies identified three begomoviruses infecting soybean and bean crops in northwestern (NW) Argentina, bean golden mosaic virus (BGMV), a virus with high capsid protein identity with Sida mottle virus (SiMoV) and a possible new viral species (isolate A). Analysis of complete DNA‐A sequences confirmed that isolate A represents a new viral species for which the authors propose the name soybean blistering mosaic virus (SbBMV), whereas the SiMoV‐like virus is actually an isolate of tomato yellow spot virus (ToYSV). Molecular hybridisation‐based detection of the three begomoviruses was accomplished using a general probe obtained by mixing full‐length DNA‐A clones of the three begomoviruses and specific probes comprising part of the common region of each viral genome. These probes were used to test samples collected in NW Argentina from 2004 through 2007. Fifty‐three percent of the bean samples were infected with BGMV, 11.5% with ToYSV and 9% with SbBMV. For soybean samples, 33% were infected with SbBMV and 18% with ToYSV. BGMV was not detected in soybean. ToYSV was also detected in the wild species Abutilon theophrasti.     

Nucleotide sequence of Chinese rape mosaic virus (oilseed rape mosaic virus), a crucifer tobamovirus infectious on Arabidopsis thaliana

The complete nucleotide sequence of Chinese rape mosaic virus has been determined. The virus is a member of the tobamovirus genus of plant virus and is able to infect Arabidopsis thaliana (L.) Heynh systemically. The analysis of the sequence shows a gene array that seems to be characteristic of crucifer tobamoviruses and which is slightly different from the one most frequently found in tobamoviruses. Based on gene organization and on comparisons of sequence homologies between members of the tobamoviruses, a clustering of crucifer tobamoviruses is proposed that groups the presently known crucifer tobamovirus into two viruses with two strains each. A name change of Chinese rape mosaic virus to oilseed rape mosaic virus is proposed.Abbreviations 2-ME 2-mercaptoethanol - EDTA ethylenediaminetetraacetic acid - SDS sodium dodecyl sulfate - UTR untranslated region - MP movement protein - CP capsid protein - CRMV Chinese rape mosaic virus - TVCV turnip vein clearing virus - PaMMV paprika mild mottle virus - PMMV-I pepper mild mottle virus (Italian isolate) - PMMV-S pepper mild mottle virus (Spanish isolate) - ToMV tomato mosaic virus - TMV tobacco mosaic virus - TMGMV tobacco mild green mosaic virus - ORSV odontoglossum ringspot virus - SHMV sunn hemp mosaic virus - CGMMV cucumber green mottle mosaic virus - ORMV oilseed rape mosaic virus     

Characterisation and genetic diversity of pepper leafroll virus,a new bipartite begomovirus infecting pepper,bean and tomato in Peru

The complete genome of a novel bipartite begomovirus (genus Begomovirus, family Geminiviridae) was cloned from a severely diseased yellow Peruvian chili pepper (Capsicum baccatum cv. Pendulum) plant collected in the department of La Libertad, Northern Peru and full‐length sequenced. The two genomic components share a common region of 156 nucleotides with a 100% sequence identity. Analysis of the genome organisation and phylogenetic comparisons revealed that the virus is a typical New World begomovirus. The closest related begomovirus, an isolate of Tomato yellow vein streak virus (ToYVSV), shared only 76.8% nucleotide sequence identity for the DNA‐A component. Therefore, following species demarcation criteria of the International Committee on Taxonomy of Viruses, this virus isolate belongs to a new begomovirus species for which the name pepper leafroll virus (PepLRV) is proposed. Pepper plants infected with the cloned PepLRV isolate developed leaf roll symptoms similar to those observed in field‐infected plants suggesting this virus as the causal agent of the disease syndrome observed in the field. Widespread occurrence of PepLRV throughout Peru was demonstrated, infecting plants of diverse cultivated species such as tomato, pepper, common and pallar beans, and of the weed species Nicandra physaloides. Low genetic diversity was observed among PepLRV isolates present in this country with no evident geographical or temporal structure of the population, typical of a recent founder effect. This is the first report of a begomovirus infecting pepper and bean crops in Peru.     

Molecular characterisation of the full-length genome of olive latent virus 1 isolated from tomato

Olive latent virus 1 (OLV-1) is a species of the Necrovirus genus. So far, it has been reported to infect olive, citrus tree and tulip. Here, we determined and analysed the complete genomic sequence of an isolate designated as CM1, which was collected from tomato plant in the Wielkopolska region of Poland and represents the prevalent isolate of OLV-1. The CM1 genome consists of monopartite single-stranded positive-sense RNA genome sized 3,699 nt with five open reading frames (ORFs) and small inter-cistronic regions. ORF1 encodes a polypeptide with a molecular weight of 23 kDa and the read-through (RT) of its amber stop codon results in ORF1 RT that encodes the virus RNA-dependent RNA polymerase. ORF2 and ORF3 encode two peptides, with 8 kDa and 6 kDa, respectively, which appear to be involved in cell-to-cell movement. ORF4 is located in the 3′ terminal and encodes a protein with 30 kDa identified as the viral coat protein (CP). The differences in CP region of four OLV-1 isolates whose sequences have been deposited in GenBank were observed. Nucleotide sequence identities of the CP of tomato CM1 isolate with those of olive, citrus and tulip isolates were 91.8%, 89.5% and 92.5%, respectively. In contrast to other OLV-1 isolates, CM1 induced necrotic spots on tomato plants and elicited necrotic local lesions on Nicotiana benthamiana, followed by systemic infection. This is the third complete genomic sequence of OLV-1 reported and the first one from tomato.     

Further evidence for the recognition of Ullucus Mild Mottle Virus as a Distinct Tobamovirus

The affinities of Ullucus mild mottle virus (UMMV). purified by a modified procedure. were examined by immunoblotting and probing with antisera to five distinct tobamoviruses. RNA. isolated from purified virus, was used for in vitro protein translation in a wheat germ system and the products examined by denaturing polyacrylamide gel electrophoresis. The results of these investigations, together with a study of the double-stranded RNAs associated with infection. confirm that UMMV is a distinct, tobamovirus which has close affinities with tobacco mosaic, tomato mosaic and cucumber green mottle tobamoviruses and more distant relationships with ribgrass mosaic and odontoglossum ringspot tobamoviruses.