• The Plant Pathology Journal
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• 제28권4호
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• pp.428-432
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• 2012

We determined the complete genome sequence of a Vietnamese isolate of Southern rice black-streaked dwarf virus (SRBSDV). Whole genome comparisons and phylogenetic analysis showed that the genome of the Vietnamese isolate shared high nucleotide sequence identities of over 97.5% with those of the reported Chinese isolates, confirming a common origin of them. Moreover, the greatest divergence between different SRBSDV isolates was found in the segments S1, S3, S4 and S6, which differs from the sequence alignment results between SRBSDV and Rice black streaked dwarf virus (RBSDV), implying that SRBSDV evolved in a unique way independent of RBSDV. This is the first report of a complete nucleotide sequence of SRBSDV from Vietnam and our data provides new clues for further understanding of molecular variation and epidemiology of SRBSDV in Southeast Asia.

• Parasites, Hosts and Diseases
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• 제57권1호
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• pp.55-60
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• 2019

This study was undertaken to determine the complete mitochondrial DNA sequence and structure of the mitochondrial genome of Spirometra ranarum, and to compare it with those of S. erinaceieuropaei and S. decipiens. The aim of this study was to provide information of the species level taxonomy of Spirometra spp. using the mitochondrial genomes of 3 Spirometra tapeworms. The S. ranarum isolate originated from Myanmar. The mitochondrial genome sequence of S. ranarum was compared with that of S. erinaceieuropaei (GenBank no. KJ599680) and S. decipiens (GenBank no. KJ599679). The complete mtDNA sequence of S. ranarum comprised 13,644 bp. The S. ranarum mt genome contained 36 genes comprising 12 protein-coding genes, 22 tRNAs and 2 rRNAs. The mt genome lacked the atp8 gene, as found for other cestodes. All genes in the S. ranarum mitochondrial genome are transcribed in the same direction and arranged in the same relative position with respect to gene loci as found for S. erinaceieuropaei and S. decipiens mt genomes. The overall nucleotide sequence divergence of 12 protein-coding genes between S. ranarum and S. decipiens differed by 1.5%, and 100% sequence similarity was found in the cox2 and nad6 genes, while the DNA sequence divergence of the cox1, nad1, and nad4 genes of S. ranarum and S. decipiens was 2.2%, 2.1%, and 2.6%, respectively.

• Journal of Veterinary Science
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• 제21권6호
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• pp.73.1-73.10
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• 2020

Background: Bovine papilloma is a neoplastic disease caused by bovine papillomaviruses (BPVs), which were recently divided into 5 genera and at least 24 genotypes. Objectives: The complete genome sequence of BPV type 15 (BPV Aks-02), a novel putative BPV type from skin samples from infected cows in Southern Xinjiang China, was determined by collecting warty lesions, followed by DNA extraction and amplicon sequencing. Methods: DNA was analyzed initially by polymerase chain reaction (PCR) using the degenerate primers FAP59 and FAP64. The complete genome sequences of the BPV Aks-02 were amplified by PCR using the amplification primers and sequencing primers. Sequence analysis and phylogenetic analysis were performed using bio-informatic software. Results: The nucleotide sequence of the L1 open reading frame (ORF) of BPV Aks-02 was 75% identity to the L1 ORF of BPV-9 reference strain from GenBank. The complete genome consisted of 7,189 base pairs (G + C content of 42.50%) that encoded 5 early (E8, E7, E1, E2, and E4) and 2 late (L1 and L2) genes. The E7 protein contained a consensus CX₂CX₂₉CX₂C zinc-binding domain and a LxCxE motif. Among the different members of this group, the percentages of the complete genome and ORFs (including 5 early and 2 late ORFs) sequence identity of BPV Aks-02 were closer to the genus Xipapillomavirus 1 of the Xipapillomavirus genus. Phylogenetic analysis and sequence similarities based on the L1 ORF of BPV Aks-02 revealed the same cluster. Conclusions: The results suggest that BPV type (BPV Aks-02) clustered with members of the Xipapillomavirus genus as BPV 15 and were closely related to Xipapillomavirus 1.

• 한국어병학회지
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• 제35권1호
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• pp.129-133
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• 2022

The full genome sequence of a Korean white spot syndrome virus (WSSV, isolate: WSSV-GoC18) is presented here. We obtained a total of 12,320,554 reads with 291,172 bases, 170 gene, and 170 coding DNA sequence, which were assembled in 1 contig. Phylogenetic analysis revealed that the WSSV-GoC18 was closely related to Chinese isolate (WSSV-PC) and distinctly different with previously reported a Korean isolate (WSSV K-LV1). The complete genome sequence of WSSV isolates will be of great help in molecular epidemiological studies, contributing to molecular diagnosis and disease prevention in shrimp aquaculture.

• 한국식물병리학회:학술대회논문집
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• 한국식물병리학회 2003년도 정기총회 및 추계학술발표회
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• pp.147.2-148
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• 2003

Complete nucleotide sequence of genome RNA of a Korean isolate of Pepper mottle virus (PepMoV-Vb) from field-collected diseased paprika (Capsicum annuum var grossum) was determined in this study. Symptoms of isolates of PepMoV were divided largely into two groups, vein banding (Vb) and vein clearing (Vc) patterns. PepMoV-Vb RNA consists of 9,640 nucleotides excluding the poly(A) tail. A single open reading frame was identified beginning at nucleotide position 169 encoding a polyprotein of 3024 amino acids which is typical of the Potyvirus genus. The complete nucleotide sequence and coding regions of PepMoV-Vb were compared to that of 11 potyviruses within the genus Potyvirus. The overall nucleotide sequence identity was 94.7 and 94.1％ identical to PepMoV-C and PepMoV-FL, respectively. Full-length cDNAs of PepMoV-Vbl were synthesized from purified viral RNAs by RT-PCR and their genome structure was analysed by RFLP analysis. This is the first report on complete nucleotide sequence of PepMoV isolated from paprika in Korea.

• 한국미생물·생명공학회지
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• 제51권4호
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• pp.559-561
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• 2023

Staphylococcus aureus is a ubiquitous pathogen associated with both human and animal diseases. In this study, we present the complete genome sequence of SA73-2, which was isolated from lettuce at an agricultural farm in South Korea. The assembled genome consists of a 2,750,304-bp circular chromosome and a 24,654-bp plasmid. This strain belongs to sequence type 188 (ST188), with spa type 189, and carries the β-lactamase gene (blaZ) on the plasmid.

• 식물병연구
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• 제22권3호
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• pp.194-197
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• 2016

Chinese yam necrotic mosaic virus (CYNMV) is one of the most widespread viruses in Chinese yam (Dioscorea opposita Thunb.) and causes serious yield losses. Currently, genetic information of CYNMV is very restricted and complete genome sequences of only two isolates (one from Japan and another from China) have been reported. In this study, we determined complete genome sequence of the CYNMV isolate AD collected from Andong, Korea. Genetic analysis of the polyprotein amino acid sequence revealed that the Korean isolate AD has high similarity with the Japanese isolate PES3 (97%) but relatively low similarity with the Chinese isolate FX1 (78%). Phylogenetic analysis using the CYNMV 3' proximal nucleotide sequences harboring the coat protein and 3' untranslated region further supported genetic relationship among the CYNMV isolates. Based on comparative analysis of the CYNMV genome sequences determined in this study and other previous studies, we generated molecular detection primers that are highly specific and efficient for CYNMV diagnosis.

• The Plant Pathology Journal
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• 제23권4호
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• pp.245-250
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• 2007

The complete genome sequence of Zucchini yellow mosaic virus stain A (ZYMV-A) isolated from a hollyhock (Althaea rosea) was determined by using RT-PCR with a series of primer sets. The virus genome consisted of 9593 nucleotides (nt), excluding the poly(A) tract at 3' terminus of the virus genome, with 5' and 3' untranslated region of 139 and 211 nt, respectively. The deduced polyprotein of ZYMV-A consisted of 3080 amino acid (aa) residues and was 351 kDa in molecular weight. All proteolytic cleavage sites of the polyprotein of ZYMV-A were compared with those of ZYMV strains, which showed the cleavage sites were conserved among ZYMV strains. The HC-Pro contained the KITC and PTK motifs, and the DAG motif was located at CP ORF of ZYMV-A, suggesting that ZYMV-A is aphid-transmissible. Phylogenetic tree analysis based on the complete genome among ZYMV strains or CP ORFs with other potyviruses showed ZYMV strains formed a distinct group. These results clearly confirmed that ZYMV-A was another distinct strain in ZYMV population at molecular level.

• 식물분류학회지
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• 제53권3호
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• pp.237-241
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• 2023

The genus Scrophularia L. (Scrophulariaceae) comprises 200-270 species worldwide and is a taxonomically challenging lineage, displaying morphological diversity and hybridization. S. kakudensis is morphologically similar to the closely related taxa S. kakudensis var. microphylla, S. pilosa, and S. cephalantha. Therefore, the purpose of this study was to sequence the chloroplast (cp) genome of S. kakudensis using next-generation sequencing and compare it to those of related taxa. The complete cp genome sequence of Scrophularia kakudensis was found to be 152,355 bp long, consisting of a pair of inverted repeats of 25,485 bp that separate a large single-copy (LSC) of 83,479 bp from small single-copy regions of 17,909 bp. The cp genome contained 78 protein-coding genes, 30 tRNAs, and four rRNAs. A phylogenetic analysis based on 78 protein-coding genes from six Scrophularia species showed S. kakudensis and S. cephalantha formed with 100% bootstrap values. We compared the complete cp genomes of S. kakudensis and S. cephalantha and identified seven sequence divergence regions: matK/rps16, rps16/trnQ, trnS/trnG, rpoB/trnC, trnS/trnG, rpl32/trnL, and ndhD/psaC. These regions may be useful for determining the phylogenetic relationships among S. kakudensis-related species.

• 한국식물병리학회:학술대회논문집
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• 한국식물병리학회 2003년도 정기총회 및 추계학술발표회
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• pp.113.1-113
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• 2003

A potexvirus, Hosta virus X (HVX-Kr), causing mosaic and mottle symptoms was isolated from hosta plants (Hosta spp.), and its entire genome RNA sequence was determined. in Korea using cDNA library and RACE methods. The genome of HVX encodes five open reading frames coding for viral replicase, triple gene block (TGB), and viral coat protein (CP) from the 5'to 3' ends, which is a typical genome structure of potexviruses. The 3-terminal region of the virus includes the TGBI (26 kDa), TGB2 (13 kDa), TGB3 (8 kDa), and 23 kDa coat protein (CP) and the 3-nontranslated region (NTR). The CP gene of the type isolate of HVX (HVX-U) was amplified by RT-PCR and its nucleotide sequence was determined. The CPs of HVX-Kr and HVX-U had 100％ and 98.9％ identical amino acids and nucleotides, respectively. Most of the regions of the genome HVX had over 50％ nucleotide identical to other sequenced potexviruses. This is the first report of complete genome sequence information of HVX and molecular evidence supporting the virus as a distinct species of the genus Potexvirus.