• Journal of Microbiology and Biotechnology
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• 제24권11호
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• pp.1490-1494
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• 2014

To probe the genomic properties of microbes thriving in desert lakes, we sequenced the full genome of a betaproteobacterial strain (SL110) belonging to the understudied genus Caenimonas of the family Comamonadaceae. This strain was isolated from a freshwater lake in the western Gobi Desert, Northern China. Its genome contains genes encoding carbon monoxide dehydrogenase, nitrate reductase, nitrite reductase, nitric oxide reductase, and sulfur oxidation enzymes, highlighting the potentially important contribution of this group of bacteria to the cycling of inorganic elements in nature. Unexpectedly, a coenzyme $F_{420}$ biosynthesis gene cluster was identified. A further search for $F_{420}$ biosynthesis gene homologs in genomic databases suggests the possible widespread presence of $F_{420}$ biosynthesis gene clusters in proteobacterial genomes.

• Genomics & Informatics
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• 제11권4호
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• pp.180-185
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• 2013

Development of liver cancers is driven largely by genomic alterations that deregulate signaling pathways, influencing growth and survival of cancer cells. Because of the hundreds or thousands of genomic/epigenomic alterations that have accumulated in the cancer genome, it is very challenging to find and test candidate genes driving tumor development and progression. Systematic studies of the liver cancer genome have become available in recent years. These studies have uncovered new potential driver genes, including those not previously known to be involved in the development of liver cancer. Novel approaches combining multiple datasets from patient tissues have created an unparalleled opportunity to uncover potential new therapeutic targets and prognostic/predictive biomarkers for personalized therapy that can improve clinical outcomes of the patients with liver cancer.

• Genomics & Informatics
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• 제7권1호
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• pp.32-37
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• 2009

The quality assurance (QA) is of utmost importance in biobanks when archived biomaterials are distributed to biomedical researchers. For sample authentication and cross-contamination detection, the two fundamental elements of QA, STR genotyping is usually utilized. However, the incorporated number of STR markers is highly redundant for biobanking purposes, resulting in time and cost inefficiency. An index to measure the cross-contamination detection capability of an STR marker, the mixture probability (MP), was developed. MP as well as other forensic parameters for STR markers was validated using STR genotyping data on 2328 normal Koreans with the commercial AmpFlSTR kit. For Koreans, 7 STR marker (D2S1338, FGA, D18S51, D8S1179, D13S317, D21S11, vWA) set was sufficient to provide discrimination power of ${\sim}10^{-10}$ and cross-contamination detection probability of ${sim}1$. Interestingly, similar marker sets were obtained from African Americans, Caucasian Americans, and Hispanic Americans under the same level of discrimination power. Only a small subset of commonly used STR markers is sufficient for QA purposes in biobanks. A procedure for selecting optimal STR markers is outlined using STR genotyping results from normal Korean population.

• Asian-Australasian Journal of Animal Sciences
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• 제14권12호
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• pp.1655-1658
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• 2001

Bovine genome samples were collected from meat of three different beef breeds (Hanwoo, Holstein and imported beef breed) that are commercially merchandized in Korean beef market. Operon B (OPB)-kits were used as random primers (3, 7, 10, 11, 12, 14) in random amplified polymorphic DNA (RAPD) method on whole genome. Each primer provided characteristic bands that were highly polymorphic. Each single primer could provide relatively efficient polymorphic band patterns among breeds. However, use of two or more primers in combination is recommended to improve resolution of experiments with higher molecular weight bands of DNA. In our experiments, OPB-11 resolved well between beef cattle breeds and Holstein. And OPB-7, 12 and 14 could be combined with OPB-11 to identify Hanwoo beef from the other two kinds of beef.

• Journal of Microbiology and Biotechnology
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• 제27권11호
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• pp.1983-1993
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• 2017

Salmonella enterica subsp. enterica serovar Typhimurium, one of the most common foodborne pathogens, is transmitted mainly through contaminated food derived from infected animals. In this study, S. Typhimurium ST1120, an isolate from pig feces in Korea, was subjected to whole-genome analysis to understand its genomic features associated with virulence. The genome of ST1120 was found to have a circular chromosome of 4,855,001 bp (GC content 52.2%) and a plasmid of 6,863 bp (GC content 46.0%). This chromosome was predicted to have 4,558 open reading frames (ORFs), 17 pseudogenes, 22 rRNA genes, and 86 tRNA genes. Its plasmid was predicted to have three ORFs. Comparative genome analysis revealed that ST1120 was phylogenetically close to S. Typhimurium U288, a critical isolate in piggery farms and food chains in Europe. In silico functional analysis predicted that the ST1120 genome harbored multiple genes associated with virulence and stress resistance, including Salmonella pathogenicity islands (SPIs containing SPI-1 to SPI-5, SPI-13, and SPI-14), C63PI locus, ST104 prophage locus, and various antibiotic resistance genes. In accordance with these analysis results, ST1120 showed competence in invasion and survival abilities when it was added to host cells. It also exhibited robust resistance against antibiotics in comparison with other S. Typhimurium strains. This is the first report of the complete genome sequence of S. Typhimurium isolated from swine in Korea. Comparative genome analysis between ST1120 and other Salmonella strains would provide fruitful information toward understanding Salmonella host specificity and developing control measures against S. Typhimurium infection.

• 한국균학회지
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• 제27권2호통권89호
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• pp.112-118
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• 1999

한국, 일본 그리고 미국 등지에서 수집된 Fusarium oxysporum f. sp. lycopersici의 electrophoretic karyotype(EK)을 분석하고자 CHEF-DRII pulsed field gel electrophoresis system(Bio-Rad Laboratories, Melville, NY)으로 각 공시균의 chromosome sized DNA를 분리하였다. EK 분석에 적합한 CHEF gel electrophoresis 조건을 얻기 위해 전기영동 시간 및 전압 그리고 switching interval 등의 조건을 다양하게 바꾸어 가며 실험하였다. 그 결과 국내 균주에서 $0.76{\sim}6.41\;Mb$에 달하는 $9{\sim}11$개의 chromosome sized DNA가 분리되었으며 그 total genome size는 $35.29{\sim}38.92\;Mb$ 이었다. 또한 일본과 미국 균주로 부터 $1.24{\sim}6.85\;Mb$범위의 $9{\sim}11$개의 chromosome sized DNA가 분리되었고 그 total genome size는 $35.32{\sim}43.87\;Mb$ 이었다. 이와 같이 얻어진 각 공시균주의 EK는 chromosome sized DNA의 length range 및 total genome size에서 국내 균주와 외국 균주간의 차이를 잘 반영하였다. 또한 국내 균주의 chromosomal polymorphism은 그 변이가 적어 서로 동일하거나 유사하였으며 외국 균주와 뚜렷이 다른 chromosomal DNA pattern을 나타냈다.

• Genomics & Informatics
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• 제12권1호
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• pp.2-11
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• 2014

After the initial enthusiasm of the human genome project, it became clear that without additional data pertaining to the epigenome, i.e., how the genome is marked at specific developmental periods, in different tissues, as well as across individuals and species-the promise of the genome sequencing project in understanding biology cannot be fulfilled. This realization prompted several large-scale efforts to map the epigenome, most notably the Encyclopedia of DNA Elements (ENCODE) project. While there is essentially a single genome in an individual, there are hundreds of epigenomes, corresponding to various types of epigenomic marks at different developmental times and in multiple tissue types. Unprecedented advances in next-generation sequencing (NGS) technologies, by virtue of low cost and high speeds that continue to improve at a rate beyond what is anticipated by Moore's law for computer hardware technologies, have revolutionized molecular biology and genetics research, and have in turn prompted innovative ways to reduce the problem of measuring cellular events involving DNA or RNA into a sequencing problem. In this article, we provide a brief overview of the epigenome, the various types of epigenomic data afforded by NGS, and some of the novel discoveries yielded by the epigenomics projects. We also provide ample references for the reader to get in-depth information on these topics.

• Journal of Plant Biotechnology
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• 제45권3호
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• pp.228-235
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• 2018

In this study, two pepper varieties, PRH1 (powdery mildew resistance line) and Saengryeg (powdery mildew resistance line), were resequenced using next generation sequencing technology in order to develop InDel markers. The genome-wide discovery of InDel variation was performed by comparing the whole-genome resequencing data of two pepper varieties to the Capsicum annuum cv. CM334 reference genome. A total of 334,236 and 318,256 InDels were identified in PRH1 and Saengryeg, respectively. The greatest number of homozygous InDels were discovered on chromosome 1 in PRH1 (24,954) and on chromosome 10 (29,552) in Saengryeg. Among these homozygous InDels, 19,094 and 4,885 InDels were distributed in the genic regions of PRH1 and Saengryeg, respectively, and 198,570 and 183,468 InDels were distributed in the intergenic regions. We have identified 197,821 polymorphic InDels between PRH1 and Saengryeg. A total of 11,697 primers sets were generated, resulting in the discovery of four polymorphic InDel markers. These new markers will be utilized in order to identify disease resistance genotypes in breeding populations. Therefore, our results will make a one-step advancement in whole genome resequencing and add genetic resource datasets in pepper breeding research.

• 식물분류학회지
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• 제51권1호
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• pp.109-114
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• 2021

Veronica nakaiana Ohwi (Plantaginaceae) is an endemic taxon on Ulleungdo Island, Korea. We report the second complete chloroplast genome sequence of V. nakaiana. Its genome size is 152,319 bp in length, comprising a large single-copy of 83,195 bp, a small single-copy of 17,702 bp, and a pair of inverted repeat regions of 25,711 bp. The complete genome contains 115 genes, including 51 protein-coding genes, four rRNA genes, and 31 tRNA genes. When comparing the two chloroplast genomes of V. nakaiana, 11 variable sites are recognized: seven SNPs and four indels. Two substitutions in the coding regions are recognized: rpoC2 (synonymous substitution) and rpl22 (nonsynonymous substitution). In nine noncoding regions, one is in the tRNA gene (trnK-UUU), one is in the intron of atpF, and seven are in the intergenic spacers (trnH-GUG~psbA, trnK-UUU, rps16~trnQ-UUG, trnC-GCA~petN, psbZ~trnG-GCC, ycf3~trnS-GGA, ycf4~cemA, and psbB~psbT). The data provide the level of genetic variation in V. nakaiana. This result will be a useful resource to formulate conservation strategies for V. nakaiana, which is a rare endemic species in Korea.

• Genomics & Informatics
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• 제9권2호
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• pp.52-58
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• 2011

Osteoporotic fracture (OF), along with bone mineral density (BMD), is an important diagnostic parameter and a clinical predictive risk factor in the assessment of osteoporosis in the elderly population. However, a genome-wide association study (GWAS) on OF has not yet been clarified sufficiently. To identify OF-associated genetic variants and candidate genes, we conducted a GWAS in a population-based cohort (Korean Association Resource [KARE], n=1,427 [case: 288 and control: 1139]) and performed a de novo replication study in hospital-based individuals (Asan and Catholic Medical Center [ACMC], n=1,082 [case: 272 and control: 810]). In a combined meta-analysis, a newly identified genetic locus in an intergenic region at 10p11.2 (near genes FZD8 and ANKRD30A ) showed the most significant association (odd ratio [OR] = 2.00, 95% confidence interval [CI] = 1.47~2.74, p=$1.27{\times}10^{-6}$) in the same direction. We provide the first evidence for a common genetic variant influencing OF and genetic information for further investigation in bone metabolism.