• The Korea Genome Conference
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• 2003.09a
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• pp.44.2-44.2
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• 2003

• Research in Plant Disease
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• v.22 no.2
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• pp.65-71
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• 2016

Cymbidium mosaic virus (CymMV) is a major virus infecting orchid plants and causing economic loss. In this study, the incidence of viral infection in Calanthe spp. at the Korean Institute of Calanthe was investigated using reverse transcription polymerase chain reaction. The CymMV infection rate was 42%, and the two viruses Odontoglossum ringspot virus and Cucumber mosaic virus had frequencies of 8% and 2%, respectively. Additionally, we characterized an isolate of CymMV, CymMV-GW, using biological tests and examined the nucleotide sequence properties of its complete genome. CymMV-GW induced chlorotic ringspots and chlorotic spot symptoms in inoculated leaves of Chenopodium amaranticolor and Nicotiana benthamiana, respectively. In this study, we have for the first complete genome sequence of CymMV-GW in Korea. The CymMV-GW genome was 6,225 nucleotides in length, excluding the poly-(A) tail, and showed whole-genome nucleotide and amino acid sequence identities of 97.7% and 100%, respectively, with the NJ-1 isolate of CymMV. Here, we report the complete genome sequence of the CymMV-GW isolate and viral infection rates for Calanthe spp. in Korea.

• Korean Journal of Microbiology
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• v.53 no.3
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• pp.227-229
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• 2017

Spirosoma rigui KCTC $12531^T$ was isolated from fresh water from the Woopo wetland, Korea. In this study, we report the complete genome sequence of a bacterium Spirosoma rigui KCTC $12531^T$, its complete genome sequence was obtained using the PacBio RS II platform. The genome comprised of 5,828,404 bp with the G + C content of 54.4%, the genome included 4,774 genes were predicted, among them, 4,647 genes are protein-coding genes.

• Molecules and Cells
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• v.23 no.2
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• pp.182-191
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• 2007

The complete mitochondrial genome of a troglobite millipede Antrokoreana gracilipes (Verhoeff, 1938) (Dipolopoda, Juliformia, Julida) was sequenced and characterized. The genome (14,747 bp) contains 37 genes (2 ribosomal RNA genes, 22 transfer RNA genes and 13 protein-encoding genes) and two large non-coding regions (225 bp and 31 bp), as previously reported for two diplopods, Narceus annularus (order Spirobolida) and Thyropygus sp. (order Spirostreptida). The A + T content of the genome is 62.1%, and four tRNAs ($tRNA^{Ser(AGN)}$, $tRNA^{Cys}$, $tRNA^{Ile}$ and $tRNA^{Met}$) have unusual and unstable secondary structures. Whereas Narceus and Thyropygus have identical gene arrangements, the $tRNA^{Thr}$ and $tRNA^{Trp}$ of Antrokoreana differ from them in their orientations and/or positions. This suggests that the Spirobolida and Spirostreptida are more closely related to each other than to the Dipolopoda. Three scenarios are proposed to account for the unique gene arrangement of Antrokoreana. The data also imply that the Duplication and Nonrandom Loss (DNL) model is applicable to the order Julida. Bayesian inference (BI) and maximum likelihood (ML) analyses using amino acid sequences deduced from the 12 mitochondrial protein-encoding genes (excluding ATP8) support the view that the three juliformian members are monophyletic (BI 100%; ML 100%), that Thyropygus (Spirostreptida) and Narceus (Spirobolida) are clustered together (BI 100%; ML 83%), and that Antrokoreana (Julida) is a sister of the two. However, due to conflict with previous reports using cladistic approaches based on morphological characteristics, further studies are needed to confirm the close relationship between Spirostreptida and Spirobolida.

• Korean Journal of Microbiology
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• v.54 no.2
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• pp.164-166
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• 2018

Salmonella enterica subsp. enterica is a foodborne pathogen that has been detected throughout the world. Here, we present the complete genome sequence of Salmonella Enteritidis isolated from a commercial kimbap that caused foodborne illness in the Republic of Korea in 2014. Complete genome sequence analysis of Salmonella Enteritidis MFDS1004839 revealed a 4,679,649 bp chromosome and a 96,994 bp plasmid, with G + C contents of 52.2% and 49.3%, respectively. The chromosome and plasmid genome included 4,482 predicted protein-coding sequences, 84 tRNAs and 22 rRNAs genes.

• Korean Journal of Microbiology
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• v.54 no.4
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• pp.465-467
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• 2018

An orange-colored, rod-shaped strain, designated Niabella ginsenosidivorans $BS26^T$, was isolated from compost. Strain $BS26^T$ showed the ability to convert major ginsenosides to minor ginsenosides, and its whole genome was sequenced. The whole genome of N. ginsenosidivorans $BS26^T$ consists of a single circular chromosome of 5,627,734 bp with 44.48% G + C content. Based on the complete genome sequence of strain $BS26^T$, we found several glycosides hydrolase-encoding genes that might involve in the conversion of major ginsenosides into minor ginsenoside and deliberate its strong pharmacological effects.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2018.04a
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• pp.43-43
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• 2018

Dumortiera hirsuta (Sw.) Nees (Dumortieraceae) is a thallose liverwort distributed in tropics and subtropics. It is the only species in family Dumortieraceae, which is the second basal family in order Marchantiales. D. hirsuta is characterized by hairy receptacles and lacking air chamber. The complete chloroplast genome of D. hirsuta was successfully rescued from raw reads generated by HiSeq4000. Its total length is 122,050 bp consisting of four regions: large single copy (LSC) region (81,697 bp), small single copy (SSC) region (20,061 bp), and two inverted repeats (IRs; 10,146 bp per each). It contained 129 genes (84 coding DNA sequence (CDS), eight rRNAs, and 37 tRNAs); 18 genes including four rRNAs, and five tRNAs are duplicated in the IR regions. The overall GC content of D. hirsuta is 28.7%, which is almost same to that of Marchantia paleacea. Phylogenetic tree based on all genes from whole chloroplast genomes will provides phylogenetic position of D. hirstua. This sequence will be an fundamental resources for further researches of order Marchantiales.

• Korean Journal of Microbiology
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• v.54 no.2
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• pp.167-168
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• 2018

Here we report the complete genome sequence of Staphylococcus xylosus S170, strong biofilm-producing strain, which comprised a single circular 2,910,005 bp chromosome and 32.97% G + C content. The genome included 2,674 protein-coding sequences, 22 rRNA genes, and 57 tRNA genes. Gene analysis of S. xylosus S170 could contribute to better understanding of biofilm-forming mechanisms.

• Korean Journal of Plant Taxonomy
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• v.51 no.2
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• pp.171-175
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• 2021

Daphne genkwa (Thymelaeaceae) is a small deciduous shrub widely cultivated as an ornamental. The complete chloroplast genome of this species is presented here. The genome is 132,741 bp long and has four subregions: 85,668 bp of large single-copy and 28,365 bp of small single-copy regions are separated by 9,354 bp of inverted repeat regions with 107 genes (71 protein-coding genes, four rRNAs, and 31 tRNAs) and one pseudogene. The phylogenetic tree shows that D. genkwa is nested within Wikstroemia and is not closely related to other species of Daphne, suggesting that it should be recognized as a species of Wikstroemia.

• Journal of Dairy Science and Biotechnology
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• v.40 no.2
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• pp.86-91
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• 2022

Chryseobacterium mulctrae KACC 21234^T is a novel species isolated from raw bovine milk. Psychrotrophic bacteria are considered contaminants and are hypothesized to originate from the environment. In this investigation, the C. mulctrae KACC 21234^T genome was determined to be 4,868,651 bp long and assembled into four contigs with a G+C ratio of 33.8%. In silico genomic analyses revealed the presence of genes encoding proteases (endopeptidase Clp, oligopeptidase b, carboxypeptidase) and lipases (phospholipase A(2), phospholipase C, acylglycerol lipase) that can catalyze the degradation of the proteins and lipids in milk, causing its quality to deteriorate. Additionally, antimicrobial resistance and putative bacteriocin genes were detected, potentially intensifying the pathogenicity of the strain. The genomic evidence presented highlights the need for improved screening protocols to minimize the potential contamination of milk by proteolytic and lipolytic psychrotrophic bacteria.