• The Plant Pathology Journal
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• v.27 no.1
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• pp.33-36
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• 2011

The genome of a potyvirus isolate associated with chlorotic spots and vein banding symptoms on Spathiphyllum spp., in Andhra Pradesh state, India was amplified by RT-PCR using degenerate potyvirus primers, amplicons cloned, and sequence (1.6 kb) analyzed. This virus isolate shared maximum identity of 74.8% and 80.2% at coat protein (CP) gene nucleotide (906 nucleotides) and amino acid (302 amino acids) levels, respectively with Dasheen mosaic virus (DsMV)-M13 isolate reported from China. But its 3'-UTR (258 nucleotides) had maximum identity of 62.5% with DsMV-Vietnam isolate. The deduced molecular weight of CP is 33.57 kDa and it contained DAG triplet in its N-terminal region. In CP amino acid based phylogenetic analysis, this virus isolate represented a separate branch but closer to DsMV isolates cluster. Based on the molecular criteria set for the discrimination of species and genus in the Potyviridae family, the present virus isolate was identified as a distinct virus species in the genus Potyvirus and proposed the name Spathiphyllum chlorotic vein banding virus (SCVbV).

• The Plant Pathology Journal
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• v.33 no.3
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• pp.296-306
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• 2017

Sugarcane mosaic virus (SCMV) is one of the most damaging viruses infecting sugarcane, maize and some other graminaceous species around the world. To investigate the genetic diversity of SCMV in Iran, the coat protein (CP) gene sequences of 23 SCMV isolates from different hosts were determined. The nucleotide sequence identity among Iranian isolates was more than 96%. They shared nucleotide identities of 75.5-99.9% with those of other SCMV isolates available in GenBank, the highest with the Egyptian isolate EGY7-1 (97.5-99.9%). The results of phylogenetic analysis suggested five divergent evolutionary lineages that did not completely reflect the geographical origin or host plant of the isolates. Population genetic analysis revealed greater between-group than within-group evolutionary divergence values, further supporting the results of the phylogenetic analysis. Our results indicated that natural selection might have contributed to the evolution of isolates belonging to the five identified SCMV groups, with infrequent genetic exchanges occurring between them. Phylogenetic analyses and the estimation of genetic distance indicated that Iranian isolates have low genetic diversity. No recombination was found in the CP cistron of Iranian isolates and the CP gene was under negative selection. These findings provide a comprehensive analysis of the population structure and driving forces for the evolution of SCMV with implications for global exchange of sugarcane germplasm. Gene flow, selection and somehow homologous recombination were found to be the important evolutionary factors shaping the genetic structure of SCMV populations.

• Biotechnology and Bioprocess Engineering:BBE
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• v.10 no.1
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• pp.29-33
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• 2005

A DNA vaccine methodology using eukaryote expression vectors to produce immunizing proteins in the vaccinated hosts is a novel approach to the development of vaccine and immuno-therapeutics, and it has achieved considerable success over several infectious diseases and various cancers. To further enhance its efficiency, attempts were made to develop novel plasmid vectors containing multiple immunostimulatory CpG motifs, for rapid and strong immune response. First, a 2.9 kb compact plasmid vector (pVAC), containing CMV promoter, polycloning site, BGH poly(A) terminator, ampicillin resistance gene and pBR322 origin was constructed. A pVAC-hEPO was also constructed, which contained a human erythropoietin gene, for evaluating the transfection efficiency of naked plasmid DNA both in vitro and in vivo. To examine the adjuvant effect of multi-CpG motifs on naked plasmid DNA, 22 and 44 enriched and unmethylated CpG motifs were introduced into pVAC to generate pVAC-ISS1 and pVAC-ISS2, respectively. $100{\mu}g$ of pSecTagB, pVAC, pVAC-ISS1 or pVAC-ISS2 were each injected intramuscularly into the tibilias anterior muscle of Balb/c mice. The level of interleukin-6 induced in the mice injected with pVAC-ISS1 and pVAC-ISS2 were significantly elevated after 12 hours, which were almost 2 and 2.5 times higher than that in the mice injected with pSecTagB, respectively. These results suggest that DNA vaccine plasmids with enriched CpG motifs can induce rapid secretion of interleukin-6 by lymphocytes. In conclusion, these vectors can contribute to the development of adjuvant-free DNA vaccinations against infectious diseases and various cancers.

• BMB Reports
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• v.38 no.6
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• pp.739-747
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• 2005

Full-length cDNA sequences of four novel SPATA4 genes in chimpanzee, cow, chicken and ascidian were identified by bioinformatic analysis using mouse or human SPATA4 cDNA fragment as electronic probe. All these genes have 6 exons and have similar protein molecular weight and do not localize in sex chromosome. The mouse SPATA4 sequence is identified as significantly changed in cryptorchidism, which shares no significant homology with any known protein in swissprot databases except for the homologous genes in various vertebrates. Our searching results showed that all SPATA4 proteins have a putative conserved domain DUF1042. The percentages of putative SPATA4 protein sequence identity ranging from 30% to 99%. The high similarity was also found in 1 kb promoter regions of human, mouse and rat SPATA4 gene. The similarities of the sequences upstream of SPATA4 promoter also have a high proportion. The results of searching SymAtlas (http://symatlas.gnf.org/SymAtlas/) showed that human SPATA4 has a high expression in testis, especially in testis interstitial, leydig cell, seminiferous tubule and germ cell. Mouse SPATA4 was observed exclusively in adult mouse testis and almost no signal was detected in other tissues. The pI values of the protein are negative, ranging from 9.44 to 10.15. The subcellular location of the protein is usually in the nucleus. And the signal peptide possibilities for SPATA4 are always zero. Using the SNPs data in NCBI, we found 33 SNPs in human SPATA4 gene genomic DNA region, with the distribution of 29 SNPs in the introns. CpG island searching gives the data about CpG island, which shows that the regions of the CpG island have a high similarity with each other, though the length of the CpG island is different from each other.This research is a fundamental work in the fields of the bioinformational analysis, and also put forward a new way for the bioinformatic analysis of other genes.

• The Plant Pathology Journal
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• v.29 no.3
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• pp.260-273
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• 2013

The incidence and distribution of Tobacco mosaic virus (TMV) and related tobamoviruses was determined using an enzyme-linked immunosorbent assay on 1,926 symptomatic horticultural crops and 107 asymptomatic weed samples collected from 78 highly infected fields in the major horticultural crop-producing areas in 17 provinces throughout Iran. The results were confirmed by host range studies and reverse transcription-polymerase chain reaction. The overall incidence of infection by these viruses in symptomatic plants was 11.3%. The coat protein (CP) gene sequences of a number of isolates were determined and disclosed to be a high identity (up to 100%) among the Iranian isolates. Phylogenetic analysis of all known TMV CP genes showed three clades on the basis of nucleotide sequences with all Iranian isolates distinctly clustered in clade II. Analysis using the complete CP amino acid sequence showed one clade with two subgroups, IA and IB, with Iranian isolates in both subgroups. The nucleotide diversity within each subgroup was very low, but higher between the two clades. No correlation was found between genetic distance and geographical origin or host species of isolation. Statistical analyses suggested a negative selection and demonstrated the occurrence of gene flow from the isolates in other clades to the Iranian population.

• Genomics & Informatics
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• v.4 no.1
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• pp.1-10
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• 2006

Epigenetic alterations are common features of human solid tumors, though global DNA methylation has been difficult to assess. Restriction Landmark Genomic Scanning (RLGS) is one of technology to examine epigenetic alterations at several thousand Notl sites of promoter regions in tumor genome. To assess sequence information for Notl sequences in RLGS gel, we cloned 1,161 unique Notl-linked clones, compromising about 60% of the spots in the soluble region of RLGS profile, and performed BLAT searches on the UCSC genome server, May 2004 Freeze. 1,023 (88%) unique sequences were matched to the CpG islands of human genome showing a large bias of RLGS toward identifying potential genes or CpG islands. The cloned Notl-loci had a high frequency (71%) of occurrence within CpG islands near the 5' ends of known genes rather than within CpG islands near the 3' ends or intragenic regions, making RLGS a potent tool for the identification of gene-associated methylation events. By mixing RLGS gels with all Notl-linked clones, we addressed 151 Notl sequences onto a standard RLGS gel and compared them with previous reports from several types of tumors. We hope our sequence information will be useful to identify novel epigenetic targets in any types of tumor genome.

• BMB Reports
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• v.37 no.6
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• pp.700-708
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• 2004

The genes located within the p74 gene region of the Choristoneura fumiferana granulovirus (ChfuGV) were identified by sequencing an 8.9 kb BamHI restriction fragment on the ChfuGV genome. The global guanine-cytosine (GC) content of this region of the genome was 33.02%. This paper presents the ORFs within the p74 gene region along with their transcriptional orientations. This region contains a total of 15 open reading frames (ORFs). Among those, 8 ORFs were found to be homologues to the baculoviral ORFs: Cf-i-p , Cf-vi, Cf-vii, Cf-viii (ubiquitin), Cf-xi (pp31), Cf-xii (lef-11), Cf-xiii (sod) and Cf-xv-p (p74). To date, no specific function has been assigned to the ORFs: Cf-i, Cf-ii, Cf-iii, Cf-iv, Cf-v, Cf-vi, Cf-vii, Cf-ix and Cf-x. The most noticeable ORFs located in this region of the ChfuGV genome were ubiquitin, lef-11, sod, fibrillin and p74. The phylogenetic trees (constructed using conceptual products of major conserved ORFs) and gene arrangement in this region were used to further examine the classification of the members of the granulovirus genus. Comparative studies demonstrated that ChfuGV along with the Cydia pomonella granulovirus (CpGV), Phthorimaea operculella granulovirus (PhopGV), Adoxophyes orana granulovirus (AoGV) and Cryptophlebia leucotreta granulovirus (ClGV) share a high degree of amino acids sequence and gene arrangement preservation within the studied region. These results support a previous report, which classified a granuloviruses into 2 distinct groups: Group I: ChfuGV, CpGV, PhopGV and AoGV and Group II: Xestia c-nigrum granulovirus (XcGV) and Plutella xylostella granulovirus (PxGV). The phylogenetic and gene arrangement studies also placed ClGV as a novel member of the Group I granuloviruses.

• Research in Plant Disease
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• v.15 no.3
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• pp.165-169
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• 2009

Twelve Cucumber mosaic virus (CMV) isolates were isolated from genetically modified (GM) and non-GM Capsicum annuum in two GM fields, Namyangju and Anseong, and their properties were investigated in this study. Coat protein (CP) gene of the CMV isolates were synthesized by RT-PCR using genus-specific primers which designed to amplify a DNA fragment of 950 bp. Purified cDNA fragments were cloned into the pGEMT easy vector for sequence determination. Nucleotide sequences (internal 657 bp) of CMV isolates were compared with Fny-CMV CP sequences and there were no significant collection site specific sequence similarities found. When predicted amino acid sequences (219 amino acids) were compared with Fny-CMV CP amino acids sequences, there were 96.8% to 97.3% similarities found from Namyangju collections and 95.9% to 96.8% similarities from Anseong collections. The phylogenetic analysis with nucleotide sequences showed definite differences in CMVs which have been isolated from the two regions.

• Proceedings of the Korean Society of Plant Pathology Conference
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• 1995.06b
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• pp.77-96
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• 1995

To obtain basic informations for the improvement of seed potato production in Korea, some etiological properties of potato virus Y(PVY) distributed in the major seed potato production area(Daekwanryeong) were characterized, and the nucleotide and amino acid sequences of the coat protein gene of the PVY strains isolated were analyzed. PVY strains in Daekwonryeong, an alpine area, were identified to be two strains, PVYo and PVYN by symptoms of indicator plants, and their distribution in potato fields was similar. Major symptom on potato varieties by PVY was grouped as either mosaic alone or mosaic accompanied with veinal necrosis in the lower leaves. The symptom occurrence of the two symptoms was similar with Irish Cobbler, but Superior showed a higher rate of mosaic symptom than the other. The PVY strain which was isolated from potato cv. Superior showing typical mosaic symptoms produced symptoms of PVY-O on the indicator plants of Chenopodium amaranticolor, Nicotiana tabacum cv. Xanthi nc and Physalis floridana, but no symptom o Capsicum annum cv. Ace. Moreover, results from the enzyme-linked immunosorbent assay with monoclonal and polyclonal antibodies showed that the isolated PVY reacts strongly with PYV-O antibodies but does not react specifically with PVY-T antibodies. The purified virus particles were flexious with a size of 730$\times$11nm. On the basis of the above characteristics, the strain was identified to be a PVY-O and named as of PVY-K strain. The flight of vector aphids was observed in late May, however, the first occurrence of infected plants was in mid June with the bait plants surrounded with PVY-infected potato plants and early July with the bait plants surrounded with PVY-free potato plants. PVY infection rates by counting symptoms on bait plants (White Burley) were 1.1% with the field surrounded with PVY-free potato plants and 13.7% the fields surrounded with PVY-infected potato plants, showing the effect of infection pressure. The propagated PVY-K strain on tobacco(N. sylvestris) was purified, and the RNA of the virus was extracted by the method of phenol extraction. The size of PVY-K RNA was measured to be 9, 500 nucleotides on agarose gel electrophoresis. The double-stranded cDNAs of PVY-K coat protein(CP) gene derived by the method of polymerase chain reaction were transformed into the competent cells of E. coli JM 109, and 2 clones(pYK6 and pYK17) among 11 clones were confirmed to contain the full-length cDNA. Purified plasmids from pYK17 were cut with Sph I and Xba I were deleted with exonuclease III and were used for sequencing analysis. The PVY-K CP gene was comprised of 801 nucleotides when counted from the clevage site of CAG(Gln)-GCA(Ala) to the stop codon of TGA and encoded 267 amino acids. The molecular weight of the encoded polypeptides was calculated to be 34, 630 daltons. The base composition of the CP gene was 33.3% of adenine, 25.2% of guanine, 20.1% of cytosine and 21.4% of uracil. The polypeptide encoded by PVY-K CP gene was comprised of 22 alanines, 20 threonines, 19 glutamic acids and 18 glycines in order. The homology of nucleotide sequence of PVY-K CP gene with those of PVY-O(Japan), PVY-T(Japan), PVY-TH(Japan), PVYN(the Netherlands), and PVYN(France) was represented as 97.3%, 88.9%, 89.3%, 89.6% and 98.5%, respectively. The amino acid sequence homology of the polypeptide encoded by PVY-K CP gene with those encoded by viruses was represented as 97.4%, 92.5%, 92.9%, 92.9%, and 98.5%, respectively.

• Proceedings of the Korean Society of Plant Pathology Conference
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• 2003.10a
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• pp.114.1-114
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• 2003

A new isolate of rod-shaped virus was identified from grafted cactus, Gymnocalycium mihanovichii grafted onto Hylocereus trigonus, in Korea. The virus proved to be a new Tobamovirus and called previously as Tobamovirus-Ca for which we suggest the name Cactus mild mottle virus(CMMoV), because it produced systemic mild mosaic symptoms on its original host. CMMoV is distantly related to known species of the genus Tobamovirus on the basis of host range, serological and sequence analyses. Western blot analysis showed that CMMoV is serologically unrelated to Summons' Opuntia virus which is the only known species of the genus found in cactus plants. The 3'-terminal 2,910 nucleotides have been sequenced for the virus. The coat protein (CP) and movement protein (MP) genes encode 161 and 306 amino acids residues, respectively. The nucleotide and amino acid sequences of the CP were 39.6 ％ to 49.2 ％ and 26.4 ％ to 40.3 ％ identical to other tobamoviruses, respectively. The MP and 3' noncoding region shared 16.3 ％ to 23.3 ％ and 44.6 ％ to 63.4 ％ identities, respectively, with the members of the genus. Phylogenetic tree analysis of the CP gene revealed that CMMoV clusters with members of subgroup I of Tobamovirus. CMMoV particles contained genomic RNA along with two subgenomic RNAs, and this characteristics is common in the members of the subgroup II. This is the first information of sequence and comparative analysis of a Tobamovirus that infects cactus.