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The first complete sequence and genome structure of daphne virus Y
Igori, D.,Hwang, U. S.,Lim, S.,Zhao, F.,Kwon, S. Y.,Moon, J. S. Springer Science + Business Media 2016 Archives of virology Vol.161 No.10
<P>From Daphne odora Thunb., an ornamental shrub in the Republic of Korea, a potyvirus was identified that has an RNA genome of 9,448 nucleotides (excluding the 3'-terminal poly(A) tail) encoding a polyprotein of 3,065 amino acids, with nine putative protease cleavage sites producing ten proteins. Since this potyvirus shared the highest nucleotide sequence identity (91 %; query coverage 5 %) with the available partial sequence of daphne virus Y (DVY) from New Zealand (EU179854), it was considered a Korean isolate of DVY. This is the first molecular characterization of the complete genome sequence of a DVY isolate.</P>
The complete sequence and genome organization of ligustrum virus A, a novel carlavirus
Igori, D.,Lim, S.,Zhao, F.,Baek, D.,Park, J. M.,Cho, H. S.,Kim, H. S.,Kwon, S. Y.,Moon, J. S. Springer Science + Business Media 2016 Archives of virology Vol.161 No.12
<P>The complete genome sequence of ligustrum virus A (LVA) from a Ligustrum obtusifolium Sieb. & Zucc. plant was determined. The genomic RNA has 8,525 nucleotides, excluding the poly(A) tail, and consists of six open reading frames typical of members of the genus Carlavirus, family Betaflexiviridae. Phylogenetic analysis of the viral replicase and coat protein (CP) indicated that LVA is closely related to daphne virus S and helenium virus. The replicase and CP of LVA shared 44.73-52.35 % and 25.39-62.46 % amino acid identity, respectively, with those of other carlaviruses. These results suggest that LVA is a member of a distinct carlavirus species.</P>
Deep Sequencing Analysis of Apple Infecting Viruses in Korea
조인숙,Davaajargal Igori,임승모,최국선,John Hammond,임현섭,문재선 한국식물병리학회 2016 Plant Pathology Journal Vol.32 No.5
Deep sequencing has generated 52 contigs derivedfrom five viruses; Apple chlorotic leaf spot virus(ACLSV), Apple stem grooving virus (ASGV), Applestem pitting virus (ASPV), Apple green crinkle associatedvirus (AGCaV), and Apricot latent virus (ApLV)were identified from eight apple samples showingsmall leaves and/or growth retardation. Nucleotide (nt)sequence identity of the assembled contigs was from68% to 99% compared to the reference sequences ofthe five respective viral genomes. Sequences of ASPVand ASGV were the most abundantly represented bythe 52 contigs assembled. The presence of the five virusesin the samples was confirmed by RT-PCR usingspecific primers based on the sequences of each assembledcontig. All five viruses were detected in threeof the samples, whereas all samples had mixed infectionswith at least two viruses. The most frequentlydetected virus was ASPV, followed by ASGV, ApLV,ACLSV, and AGCaV which were withal found inmixed infections in the tested samples. AGCaV wasidentified in assembled contigs ID 1012480 and 93549,which showed 82% and 78% nt sequence identity withORF1 of AGCaV isolate Aurora-1. ApLV was identifiedin three assembled contigs, ID 65587, 1802365,and 116777, which showed 77%, 78%, and 76% ntsequence identity respectively with ORF1 of ApLVisolate LA2. Deep sequencing assay was shown to bea valuable and powerful tool for detection and identificationof known and unknown virome in infectedapple trees, here identifying ApLV and AGCaV incommercial orchards in Korea for the first time.
Lim, Seungmo,Igori, Davaajargal,Yoo, Ran Hee,Zhao, Fumei,Cho, In-Sook,Choi, Gug-Seoun,Lim, Hyoun-Sub,Lee, Su-Heon,Moon, Jae Sun M. Nijhoff ; Kluwer Academic Publishers 2015 Virus genes Vol.51 No.2
<P>A peach tree (Prunus persica) showing yellowing and mild mottle symptoms was analyzed using high-throughput RNA sequencing to determine the causal agent. A total of nine contigs similar to Little cherry virus 1 (LChV-1) were produced, and all the contigs showed nucleotide sequence identity (lower than 83??%) and query coverage (higher than 73??%) with LChV-1. The symptomatic peach sample was confirmed to be infected with LChV-1-like virus as a result of reverse transcription-polymerase chain reaction using primers designed based on sequences of the contigs. Occurrence of diseases caused by LChV-1 in Prunus species has been reported. Complete 16,931-nt genome of the peach virus composed of eight open reading frames was determined, and conserved domains including viral methyltransferase, viral helicase 1, RNA-dependent RNA polymerase (RdRp), heat shock protein 70 homologue (HSP70h), HSP90h and closterovirus coat protein (CP) were identified. Phylogenetic trees based on amino acid sequence alignments between the peach virus and members in the family Closteroviridae showed that the virus was most similar to LChV-1. Pairwise comparisons based on amino acid sequence alignments of three genes (RdRp, HSP70h and CP) between the peach virus and LChV-1 isolates showed the highest amino acid sequence identities, with 84.32??% for RdRp, 85.48??% for HSP70h and 80.45??% for CP. These results indicate that this is the first report for the presence of LChV-1 in South Korea and may be one of the first reports of natural infection of peach by LChV-1. Although it is not clear if LChV-1 YD isolate was responsible for specific symptoms observed, detection and characterization of the peach tree-infecting LChV-1 in South Korea would be useful in terms of the epidemiology of LChV-1.</P>
Zhao, F.,Lim, S.,Igori, D.,Yoo, R.H.,Kwon, S.Y.,Moon, J.S. Academic Press 2016 Virology Vol.492 No.-
<P>We report here the development of tobacco ringspot virus (TRSV)-based vectors for the transient expression of foreign genes and for the analysis of endogenous gene function in plants using virus induced gene silencing. The jellyfish green fluorescent protein (GFP) gene was inserted between the TRSV movement protein (MP) and coat protein (CP) regions, resulting in high in-frame expression of the RNA2-encoded viral polyprotein. GFP was released from the polyprotein via an N-terminal homologous MP-CP cleavage site and a C-terminal foot-and-mouth disease virus (FMDV) 2 A catalytic peptide in Nicotiana benthamiana. The VIGS target gene was introduced in the sense and antisense orientations into a SnaBI site, which was created by mutating the sequence following the CP stop codon. VIGS of phytoene desaturase (PDS) in N. benthamiana, Arabidopsis ecotype Col-0, cucurbits and legumes led to obvious photo-bleaching phenotypes. A significant reduction in PDS mRNA levels in silenced plants was confirmed by semi-quantitative RT-PCR. (C) 2016 Elsevier Inc. All rights reserved.</P>