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characterization of the genome of rice tungro bacilliform virus: comparison with commelina yellow mottle virus and caulimoviruses.rice tungro disease is caused by an infection of two different viruses, rice tungro spherical virus (a (+) sense rna virus) and rice tungro bacilliform virus (rtbv) with a genome of circular double-stranded dna. the genome of an rtbv isolate from the philippines was cloned, sequenced, and found to be 8000 bp in length. it contains four open reading frames (orfs) on a single strand, with orf 1 having an internal termination codon (taa). the 5' and 3' ends of a polyadenylated viral rna transcript, ...19911926781
rice tungro disease is caused by an rna and a dna virus.we present evidence that rice tungro spherical virus (rtsv) has a genome of polyadenylated single-stranded rna of about 10 kb whereas rice tungro bacilliform virus (rtbv) contains double-stranded circular dna. rtbv dna has been mapped and shown to have two discontinuities, one in each strand, at specific sites; it thus resembles that of the caulimoviruses. gel electrophoresis of rtsv preparations revealed two protein bands (mr 35k and 26k). rtbv yielded two major protein bands of 37k and 33k tog ...19912016590
molecular cloning and sequencing of coat protein-encoding cdna of rice tungro spherical virus--a plant picornavirus.rice tungro spherical virus (rtsv) was shown to have three coat protein (cp) species by high resolution nadodso4-page and western blot analyses. the sequence of a coat protein-expressing cdna clone that was identified and selected from a rtsv cdna library showed that the insert was composed of 2823 bp with only one large open reading frame (orf) coding for 941 amino acids. the positions of the three coat proteins were located in the putative polyprotein by n-terminal microsequencing and were sho ...19938367940
nucleotide sequence and genomic organization of rice tungro spherical virus.rice tungro disease is caused by a combination of two viruses: rice tungro spherical virus (rtsv) and rice tungro bacilliform virus (jones et al. (1991) j. gen. virol. 72, 757-761.). the genome of rtsv is a single-stranded polyadenylated rna. we present here the 12,433-nucleotide complete sequence of rtsv genomic rna and its deduced coding regions. this sequence contains a large open reading frame (orf) which initiates following a 514-nucleotide 5' leader sequence and is capable of encoding a vi ...19938460478
immunological characterization of rice tungro spherical virus coat proteins and differentiation of isolates from the philippines and india.rice tungro spherical virus (rtsv) has an rna genome of more than 12 kb with various features which classify it as a plant picornavirus. the capsid comprises three coat protein (cp) species, cp1, cp2 and cp3, with predicted molecular masses of 22.5, 22.0 and 33 kda, respectively, which are cleaved from a polyprotein. in order to obtain information on the properties of these proteins, each was expressed in e. coli, purified as a fusion to the maltose-binding protein and used for raising a polyclo ...19968760450
detection of rice tungro bacilliform virus in field and glasshouse samples from india using the polymerase chain reaction.rice tungro bacilliform virus (rtbv) together with rice tungro spherical virus (rtsv) is the causal agent for the rice tungro disease. a rapid technique was developed to detect rtbv dna in the crude extract of freshly collected leaf samples by polymerase chain reaction (pcr). this technique can detect the viral dna in 1000-fold diluted leaf extract. detection has been possible in samples stored upto 5 days after the collection. this technique may have wide application for the field diagnosis of ...19968783150
rice tungro spherical virus: nucleotide sequence of the 3' genomic half and studies on the two small 3' open reading frames.rice tungro spherical virus (rtsv) consists of a single-stranded rna genome of about 12 kilobases that contains one large open reading frame, orf 1 and two small orfs 2 and 3 at its 3' end (shen et al., 1993, virology 193:621-630); it was suggested that orf 2 was expressed via a frameshift. to study the genomic information of rtsv and the variation between different rtsv isolates, the 3' half of a philippine isolate and parts of a thai and an indian isolate were cloned and sequenced. significant ...19969035368
sequences of the three coat protein genes of a malaysian isolate of rice tungro spherical virus reveal a close relationship to the philippine isolate.coat protein genes cp1, cp2 and cp3 of an isolate (map1) of rice tungro spherical virus (rtsv) from malaysia were isolated, cloned and sequenced. comparative analysis indicated that map1 isolate is closely related to the philippine isolate.19979354271
variation in coat protein genes among five geographically different isolates of rice tungro spherical virus.the variation in the sequence of the coat protein genes of four isolates of rice tungro spherical virus from different countries, malaysia, thailand, india and bangladesh, was compared with an isolate from the philippines. the evidence from rt-pcr, southern blot hybridization and sequences of the coat protein genes indicated that the isolates appeared to fall into two groups. one comprised the philippine and malaysian isolates (about 95% sequence similarity) and the other the bangladeshi and ind ...19979672645
rice tungro spherical virus polyprotein processing: identification of a virus-encoded protease and mutational analysis of putative cleavage sites.rice tungro spherical virus encodes a large polyprotein containing motifs with sequence similarity to viral serine-like proteases and rna polymerases. polyclonal antisera raised against domains of the putative protease and polymerase in fusion with glutathione s-transferase detected a protein of about 35 kda and, in very low amounts, a protein of about 70 kda, respectively, in extracts from infected plants. in in vitro transcription/translation systems and in escherichia coli we demonstrated a p ...19989683576
original reverse transcription polymerase chain reaction method to obtain the full-length cdna of rice tungro spherical virus.a two-step reverse transcription reaction combined with long pcr was developed in order to obtain the full-length cdna from the 12.2 kbp genomic rna of rice tungro spherical virus. a first step reverse transcription, performed at 45 degrees c using a reverse transcriptase deprived of rnase h activity, allowed the synthesis of a nearly full-length cdna of 11.7 kbp. a second step reaction, carried out at 65 degrees c using a thermostable polymerase, was necessary to destabilise secondary structure ...199910381086
complete nucleotide sequence of the rice tungro spherical virus genome of the highly virulent strain vt6.the complete nucleotide sequence of rice tungro spherical virus (rtsv) strain vt6, originally from mindanao, the philippines, with higher virulence to resistant rice cultivars, was determined and compared with the published sequence for the philippine-type strain a (rtsv-a-shen). it was reported that rtsv-a was not able to infect a rice resistant cultivar tkm 6 (10). rtsv-vt6 and rtsv-a-shen share 90% and 95% homology at nucleotide and amino-acid levels, respectively. the n-terminal leader seque ...200010766310
genetic diversity of rice tungro spherical virus in tungro-endemic provinces of the philippines and indonesia.the two adjacent genes of coat protein 1 and 2 of rice tungro spherical virus (rtsv) were amplified from total rna extracts of serologically indistinguishable field isolates from the philippines and indonesia, using reverse transcriptase polymerase chain reaction (rt-pcr). digestion with hindiii and bstyi restriction endonucleases differentiated the amplified dna products into eight distinct coat protein genotypes. these genotypes were then used as indicators of virus diversity in the field. int ...200010948991
genetic composition and complexity of virus populations at tungro-endemic and outbreak rice sites.we have recently demonstrated the geographic isolation of rice tungro bacilliform virus (rtbv) populations in the tungro-endemic provinces of isabela and north cotabato, philippines. in this study, we examined the genetic structure of the virus populations at the tungro-outbreak sites of lanao del norte, a province adjacent to north cotabato. we also analyzed the virus populations at the tungro-endemic sites of subang, indonesia, and dien khanh, vietnam. total dna extracts from 274 isolates were ...200011205110
characterization and complete nucleotide sequence of strawberry mottle virus: a tentative member of a new family of bipartite plant picorna-like viruses.an isolate of strawberry mottle virus (smov) was transferred from fragaria vesca to nicotiana occidentalis and chenopodium quinoa by mechanical inoculation. electron micrographs of infected tissues showed the presence of isometric particles of approximately 28 nm in diameter. smov-associated tubular structures were also conspicuous, particularly in the plasmodesmata of c. quinoa. dsrna extraction of smov-infected n. occidentalis yielded two bands of 6.3 and 7.8 kbp which were cloned and sequence ...200211752720
characterization of a protein from rice tungro spherical virus with serine proteinase-like activity.the rna genome of rice tungro spherical virus (rtsv) is predicted to be expressed as a large polyprotein precursor (shen et al., virology 193, 621-630, 1993 ). the polyprotein is processed by at least one virus-encoded protease located adjacent to the c-terminal putative rna polymerase which shows sequence similarity to viral serine-like proteases. the catalytic activity of this protease was explored using in vitro transcription/translation systems. besides acting in cis, the protease had activi ...200212466496
detection of molecular variability in rice tungro bacilliform viruses from india using polymerase chain reaction-restriction fragment length polymorphism.rice tungro bacilliform virus (rtbv) with rice tungro spherical virus (rtsv) causes the destructive tungro disease of rice. in order to ascertain the molecular variability of rtbv in india, primers were designed to amplify a polymorphic dna fragment of the virus. polymerase chain reaction-restriction fragment length polymorphism (pcr-rflp) analysis on a number of field isolates indicated mixed infections and molecular heterogeneity in the viral genome.200312668273
changes in level of virus accumulation and incidence of infection are critical in the characterization of rice tungro bacilliform virus (rtbv) resistance in rice.analysis by enzyme-linked immunosorbent assay showed that rice tungro bacilliform virus (rtbv) accumulated in a cyclic pattern from early to late stages of infection in tungro-susceptible variety, taichung native 1 (tn1), and resistant variety, balimau putih, singly infected with rtbv or co-infected with rtbv + rice tungro spherical virus (rtsv). these changes in virus accumulation resulted in differences in rtbv levels and incidence of infection. the virus levels were expressed relative to thos ...200312898326
molecular biology of rice tungro viruses.rice tungro, the most important virus disease of rice in south and southeast asia, is caused by a complex of two viruses, rice tungro bacilliform virus (rtbv) and rice tungro spherical virus (rtsv). rtbv is a plant pararetrovirus with bacilliform particles, the structure of which is based on t = 3 icosahedral symmetry cut across the threefold axis.the particles encapsidate a circular double-stranded dna of 8 kbp that encodes four proteins. the current information on the properties, functions, an ...199615012544
3c-like protease encoded by rice tungro spherical virus is autocatalytically processed.the 3c-protease of rice tungro spherical virus (rtsv) was previously identified as a cis- and trans-acting protease. in vitro translation of the protease resulted in several protein products, demonstrating that the protease is cleaved by itself. the protease was then produced in escherichia coli as a fusion protein with maltose-binding protein (mbp). two forms of the protease were purified after mbp affinity chromatography in the column buffer. after analyses of the purified proteins, we specula ...200515503215
multiplex rt-pcr, a novel technique for the simultaneous detection of the dna and rna viruses causing rice tungro disease.rice tungro, economically the most important viral disease of rice, is a complex disease caused by two morphologically and genomically dissimilar viruses, rice tungro bacilliform virus (rtbv), a double stranded dna virus replicating through rna intermediate and rice tungro spherical virus (rtsv), a single stranded rna virus with 3' poly (a) tail. a novel multiplex rt-pcr technique for the simultaneous detection of rtbv and rtsv from the total rna extracted from tungro-infected plants has been de ...200616490261
a novel approach for developing resistance in rice against phloem limited viruses by antagonizing the phloem feeding hemipteran vectors.rice production is known to be severely affected by virus transmitting rice pests, brown planthopper (bph) and green leafhopper (glh) of the order hemiptera, feeding by phloem abstraction. asal, a novel lectin from leaves of garlic (allium sativum) was previously demonstrated to be toxic towards hemipteran pests when administered in artificial diet as well as in asal expressing transgenic plants. in this report asal was targeted under the control of phloem-specific agrobacterium rolc and rice su ...200616941213
sequence analysis of the complete genomes of two rice tungro spherical virus isolates from india. 200717122897
rna-interference in rice against rice tungro bacilliform virus results in its decreased accumulation in inoculated rice plants.rice tungro is a viral disease seriously affecting rice production in south and southeast asia. tungro is caused by the simultaneous infection in rice of rice tungro bacilliform virus (rtbv), a double-stranded dna virus and rice tungro spherical virus (rtsv), a single-stranded rna virus. to apply the concept of rna-interference (rnai) for the control of rtbv infection, transgenic rice plants expressing dna encoding orf iv of rtbv, both in sense as well as in anti-sense orientation, resulting in ...200818306054
near immunity to rice tungro spherical virus achieved in rice by a replicase-mediated resistance strategy.abstract rice tungro disease is caused by rice tungro bacilliform virus (rtbv), which is responsible for the symptoms, and rice tungro spherical virus (rtsv), which assists transmission of both viruses by leafhoppers. transgenic japonica rice plants (oryza sativa) were produced containing the rtsv replicase (rep) gene in the sense or antisense orientation. over 70% of the plants contained one to five copies of the rep gene, with integration occurring at a single locus in most cases. plants produ ...199918944657
transgenic expression of coat protein gene of rice tungro bacilliform virus in rice reduces the accumulation of viral dna in inoculated plants.rice tungro, a devastating disease of rice in south and southeast asia, is caused by the joint infection of rice tungro bacilliform virus (rtbv) and rice tungro spherical virus (rtsv). in order to obtain transgenic resistance against rtbv, indica rice cultivar pusa basmati-1 was transformed to express the coat protein (cp) gene of an indian isolate of rtbv. rice plants containing the transgene integrated in low copy numbers were obtained, in which the cp was shown to accumulate in the leaf tissu ...200919387813
suppression of two tungro viruses in rice by separable traits originating from cultivar utri merah.rice tungro disease (rtd) is caused by rice tungro spherical virus (rtsv) and rice tungro bacilliform virus (rtbv) transmitted by green leafhoppers. rice cv. utri merah is highly resistant to rtd. to define the rtd resistance of utri merah, near-isogenic lines (nil, bc(5) or bc(6)) developed from utri merah and susceptible cv. taichung native 1 (tn1) were evaluated for reactions to rtsv and rtbv. tw16 is an nil (bc(5)) resistant to rtd. rtbv was able to infect both tn1 and tw16 but the levels of ...200919737100
single nucleotide polymorphisms in a gene for translation initiation factor (eif4g) of rice (oryza sativa) associated with resistance to rice tungro spherical virus.rice tungro disease (rtd) is a serious constraint to rice production in south and southeast asia. rtd is caused by rice tungro spherical virus (rtsv) and rice tungro bacilliform virus. rice cv. utri merah is resistant to rtsv. to identify the gene or genes involved in rtsv resistance, the association of genotypic and phenotypic variations for rtsv resistance was examined in backcross populations derived from utri merah and rice germplasm with known rtsv resistance. genetic analysis revealed that ...201019958136
genome-wide analysis of nac transcription factor family in rice.we investigated 151 non-redundant nac genes in rice and 117 in arabidopsis. a complete overview of this gene family in rice is presented, including gene structures, phylogenies, genome localizations, and expression profiles. we also performed a comparative analysis of these genes in rice and arabidopsis. conserved amino acid residues and phylogeny construction using the nac conserved domain sequence suggest that osnac gene family was classified broadly into two major groups (a and b) and sixteen ...201020600702
molecular detection of nine rice viruses by a reverse-transcription loop-mediated isothermal amplification assay.a reverse-transcription loop-mediated isothermal amplification (rt-lamp) assay was established for the detection of nine viruses from infected rice plants, including rice black-streaked dwarf virus (rbsdv), rice dwarf virus (rdv), rice gall dwarf virus (rgdv), rice ragged stunt virus (rrsv), rice transitory yellowing virus (rtyv), rice stripe virus (rsv), rice grassy stunt virus (rgsv), rice tungro spherical virus (rtsv), and rice tungro bacilliform virus (rtbv). virus-specific primer sets were ...201020837064
gene structures, classification and expression models of the ap2/erebp transcription factor family in rice.we identified 163 ap2/erebp (apetala2/ethylene-responsive element-binding protein) genes in rice. we analyzed gene structures, phylogenies, domain duplication, genome localizations and expression profiles. conserved amino acid residues and phylogeny construction using the ap2/erf conserved domain sequence suggest that in rice the osap2/erebp gene family can be classified broadly into four subfamilies [ap2, rav (related to abi3/vp1), dreb (dehydration-responsive element-binding protein) and erf ( ...201021169347
short orf-dependent ribosome shunting operates in an rna picorna-like virus and a dna pararetrovirus that cause rice tungro disease.rice tungro disease is caused by synergistic interaction of an rna picorna-like virus rice tungro spherical virus (rtsv) and a dna pararetrovirus rice tungro bacilliform virus (rtbv). it is spread by insects owing to an rtsv-encoded transmission factor. rtbv has evolved a ribosome shunt mechanism to initiate translation of its pregenomic rna having a long and highly structured leader. we found that a long leader of rtsv genomic rna remarkably resembles the rtbv leader: both contain several short ...201222396650
expression and the antigenicity of recombinant coat proteins of tungro viruses expressed in escherichia coli.rice tungro disease (rtd) is a recurring disease affecting rice farming especially in the south and southeast asia. the disease is commonly diagnosed by visual observation of the symptoms on diseased plants in paddy fields and by polymerase chain reaction (pcr). however, visual observation is unreliable and pcr can be costly. high-throughput as well as relatively cheap detection methods are important for rtd management for screening large number of samples. due to this, detection by serological ...201727923590
evaluation of virus resistance and agronomic performance of rice cultivar asd 16 after transfer of transgene against rice tungro bacilliform virus by backcross breeding.severe losses of rice yield in south and southeast asia are caused by rice tungro disease (rtd) induced by mixed infection of rice tungro bacilliform virus (rtbv) and rice tungro spherical virus (rtsv). in order to develop transgene-based resistance against rtbv, one of its genes, orf iv, was used to generate transgenic resistance based on rna-interference in the easily transformed rice variety pusa basmati-1, and the transgene was subsequently introgressed to rice variety asd 16, a variety popu ...201626983604
rice tungro spherical virus resistance into photoperiod-insensitive japonica rice by marker-assisted selection.rice tungro disease (rtd) is one of the destructive and prevalent diseases in the tropical region. rtd is caused by rice tungro spherical virus (rtsv) and rice tungro bacilliform virus. cultivation of japonica rice (oryza sativa l. ssp japonica) in tropical asia has often been restricted because most japonica cultivars are sensitive to short photoperiod, which is characteristic of tropical conditions. japonica1, a rice variety bred for tropical conditions, is photoperiod-insensitive, has a high ...201526366118
creation of transgenic rice plants producing small interfering rna of rice tungro spherical virus.rice tungro spherical virus (rtsv), also known as rice waika virus, does not cause visible symptoms in infected rice plants. however, the virus plays a critical role in spreading rice tungro bacilliform virus (rtbv), which is the major cause of severe symptoms of rice tungro disease. recent studies showed that rna interference (rnai) can be used to develop virus-resistance transgenic rice plants. in this report, we presented simple procedures and protocols needed for the creation of transgenic r ...201525984767
suppression of cell wall-related genes associated with stunting of oryza glaberrima infected with rice tungro spherical virus.rice tungro disease is a complex disease caused by the interaction between rice tungro bacilliform virus and rice tungro spherical virus (rtsv). rtsv alone does not cause recognizable symptoms in most asian rice (oryza sativa) plants, whereas some african rice (o. glaberrima) plants were found to become stunted by rtsv. stunting of rice plants by virus infections usually accompanies the suppression of various cell wall-related genes. the expression of cell wall-related genes was examined in o. g ...201424550897
delay in virus accumulation and low virus transmission from transgenic rice plants expressing rice tungro spherical virus rna.rice tungro, a devastating viral disease of rice in south and southeast asia, is caused by the joint infection of a dna virus, rice tungro bacilliform virus (rtbv) and an rna virus rice tungro spherical virus (rtsv). rtbv and rtsv are transmitted exclusively by the insect vector green leafhopper (glh). rtsv is necessary for the transmission of rtbv. to obtain transgenic resistance against rtsv, indica rice plants were transformed using dna constructs designed to express an untranslatable sense o ...201222826155
the molecular diversity and evolution of rice tungro bacilliform virus from indian perspective.rice tungro disease is caused by a combination of two viruses: rice tungro spherical virus and rice tungro bacilliform virus (rtbv). this study was performed with the objective to decipher the molecular variability and evolution of rtbv isolates present in the tungro-affected states of indian subcontinent. phylogenetic analysis based on orf-i, orf-ii, and orf-iv sequences showed distinct divergence of indian rtbv isolates into two groups; one consisted isolates from hyderabad (andhra pradesh), c ...201222544477
development of sybr green i based real-time pcr assays for quantitative detection of rice tungro bacilliform virus and rice tungro spherical virus.rice tungro disease, caused by simultaneous infection of rice tungro bacilliform virus (rtbv) and rice tungro spherical virus (rtsv), is an important cause of reduced rice harvests in south and southeast asia. although various biological, serological and molecular techniques have been reported previously for the detection of rtbv and rtsv, a method that determines accurately the exact viral load in a tungro affected plant is still not available. the present study describes a method for the absol ...201222326276
genetic variation of coat protein gene among the isolates of rice tungro spherical virus from tungro-endemic states of the india.rice tungro disease, one of the major constraints to rice production in south and southeast asia, is caused by a combination of two viruses: rice tungro spherical virus (rtsv) and rice tungro bacilliform virus (rtbv). the present study was undertaken to determine the genetic variation of rtsv population present in tungro endemic states of indian subcontinent. phylogenetic analysis based on coat protein sequences showed distinct divergence of indian rtsv isolates into two groups; one consisted is ...201222234819
identification of a maize chlorotic dwarf virus silencing suppressor protein.maize chlorotic dwarf virus (mcdv), a member of the genus waikavirus, family secoviridae, has a 11784 nt (+)ssrna genome that encodes a 389kda proteolytically processed polyprotein. we show that the n-terminal 78kda polyprotein (r78) of mcdv acts as a suppressor of rna silencing in a well-established assay system. we further demonstrate that r78 is cleaved by the viral 3c-like protease into 51 and 27kda proteins (p51 and p27), and that p51 is responsible for silencing suppressor activity. silenc ...201728160664
complete genome sequence of bellflower vein chlorosis virus, a novel putative member of the genus waikavirus.the complete genome sequence of a new virus isolated from a bellflower (campanula takesimana) plant was determined. the genome of this virus is composed of monopartite single-stranded rna of 11,649 nucleotides in length. blast searches of protein databases showed that the encoded polyprotein has a maximum amino acid sequence identity of 42% (with 99% coverage) to the polyprotein of the isolate orissa of rice tungro spherical virus (rtsv; genus waikavirus). phylogenetic analysis strongly supports ...201526370789
the complete genome sequence of a south indian isolate of rice tungro spherical virus reveals evidence of genetic recombination between distinct isolates.in this study, complete genome of a south indian isolate of rice tungro spherical virus (rtsv) from andhra pradesh (ap) was sequenced, and the predicted amino acid sequence was analysed. the rtsv rna genome consists of 12,171 nt without the poly(a) tail, encoding a putative typical polyprotein of 3,470 amino acids. furthermore, cleavage sites and sequence motifs of the polyprotein were predicted. multiple alignment with other rtsv isolates showed a nucleotide sequence identity of 95% to east ind ...201323925555
gene expression responses to rice tungro spherical virus in susceptible and resistant near-isogenic rice plants.rice cultivar taichung native 1 (tn1) is susceptible to rice tungro spherical virus (rtsv). tw16 is a backcross line developed between tn1 and rtsv-resistant cultivar utri merah. rtsv accumulation in tw16 was significantly lower than in tn1, although both tn1 and tw16 remained asymptomatic. we compared the gene expression profiles of tn1 and tw16 infected by rtsv to identify the gene expression patterns accompanying the accumulation and suppression of rtsv. about 11% and 12% of the genes in the ...201323183448
ictv virus taxonomy profile: secoviridae.members of the family secoviridae are non-enveloped viruses with mono- or bipartite (rna-1 and rna-2) linear positive-sense ssrna genomes with the size of the rnas combined ranging from 9 to 13.7 kb. they are related to picornaviruses and are classified in the order picornavirales. the majority of known members infect dicotyledonous plants and many are important plant pathogens (e.g. grapevine fanleaf virus and rice tungro spherical virus). this is a summary of the current international committe ...201728452295
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