• Food Science of Animal Resources
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• v.33 no.6
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• pp.715-722
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• 2013

Heugu (Korea Black Cattle) is one of the indigenous cattle breeds in Korea; however there has been severe lack of genomic studies on the breed. In this study, we report the first whole genome resequencing of Heugu at higher sequence coverage using Illumina HiSeq 2000 platform. More than 153.6 Giga base pairs sequence was obtained, of which 97% of the reads were mapped to the bovine reference sequence assembly (UMD 3.1). The number of non-redundantly mapped sequence reads corresponds to approximately 28.9-fold coverage across the genome. From these data, we identified a total of over six million single nucleotide polymorphisms (SNPs), of which 29.4% were found to be novel using the single nucleotide polymorphism database build 137. Extensive annotation was performed on all the detected SNPs, showing that most of SNPs were located in intergenic regions (70.7%), which is well corresponded with previous studies. Of the total SNPs, we identified substantial numbers of non-synonymous SNPs (13,979) in 5,999 genes, which could potentially affect meat quality traits in cattle. These results provide genome-wide SNPs that can serve as useful genetic tools and as candidates in searches for phenotype-altering DNA difference implicated with meat quality traits in cattle. The importance of this study can be further pronounced with the first whole genome sequencing of the valuable local genetic resource to be used in further genomic comparison studies with diverse cattle breeds.

• Genomics & Informatics
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• v.15 no.4
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• pp.136-141
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• 2017

Accurate detection of genomic alterations, especially druggable hotspot mutations in tumors, has become an essential part of precision medicine. With targeted sequencing, we can obtain deeper coverage of reads and handle data more easily with a relatively lower cost and less time than whole-exome or whole-genome sequencing. Recently, we designed a customized gene panel for targeted sequencing of major solid cancers. In this study, we aimed to validate its performance. The cancer panel targets 95 cancer-related genes. In terms of the limit of detection, more than 86% of target mutations with a mutant allele frequency (MAF) <1% can be identified, and any mutation with >3% MAF can be detected. When we applied this system for the analysis of Acrometrix Oncology Hotspot Control DNA, which contains more than 500 COSMIC mutations across 53 genes, 99% of the expected mutations were robustly detected. We also confirmed the high reproducibility of the detection of mutations in multiple independent analyses. When we explored copy number alterations (CNAs), the expected CNAs were successfully detected, and this result was confirmed by target-specific genomic quantitative polymerase chain reaction. Taken together, these results support the reliability and accuracy of our cancer panel in detecting mutations. This panel could be useful for key mutation profiling research in solid tumors and clinical translation.

• Korean Journal of Breeding Science
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• v.43 no.2
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• pp.103-114
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• 2011

In recent years, genomic resources and information have accumulated at an ever increasing pace, in many plant species, through whole genome sequencing, large scale analysis of transcriptomes, DNA markers and functional studies of individual genes. Well-characterized species within key plant taxa, co-called "model systems", have played a pivotal role in nucleating the accumulation of genomic information and databases, thereby providing the basis for comparative genomic studies. In addition, recent advances to "Next Generation" sequencing technologies have propelled a new wave of genomics, enabling rapid, low cost analysis of numerous genomes, and the accumulation of genetic diversity data for large numbers of accessions within individual species. The resulting wealth of genomic information provides an opportunity to discern evolutionary processes that have impacted genome structure and the function of genes, using the tools of comparative analysis. Comparative genomics provides a platform to translate information from model species to crops, and to relate knowledge of genome function among crop species. Ultimately, the resulting knowledge will accelerate the development of more efficient breeding strategies through the identification of trait-associated orthologous genes and next generation functional gene-based markers.

• Proceedings of the Korean Society of Life Science Conference
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• 2000.06a
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• pp.3-8
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• 2000

The complete genome sequence of a Gram-positive bacterium .Bacillus subtilis has recently been reported and it is now clear that more than 50% of its ORFs have no known function (1). To study the global gene expression in B. subtilis at single gene resolution, we have tested the glass DNA microarrays in a step-wise fashion. As a preliminary experiment, we have created arrays of PCR products for 14 ORF whose transcription patterns have been well established through transcriptional mapping analysis. We measured changes in mRNA transcript levels between early exponential and stationary phase by hybridizing fluorescently labeled cDNA (with Cy3-UTP and Cy5-UTP) onto the array. We then compared the microarray data to confirm that the transcription patterns of these genes are well consistent with the known Northern analysis data. Since the preliminary test has been successful, we scaled up the experiments to ${\sim}$94% of the 4,100 annotated ORFs for the complete genome sequence of B. subtilis. Using this whole genomic microarray, we searched genes that are catabolite-repressive and those that are under the control of ${\sigma}^{Y}$, one of the functionally unknown ECF sigma factors. From these results, we here report that we have established DNA microarray techniques that are applicable for the whole genome of B. subtilis.

• Journal of Microbiology and Biotechnology
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• v.23 no.4
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• pp.459-466
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• 2013

The lactic acid bacterium Streptococcus thermophilus is widely used as a starter culture for the production of dairy products. Whole-genome sequencing is expected to utilize the genetic basis behind the metabolic functioning of lactic acid bacterium (LAB), for development of their use in biotechnological and probiotic applications. We sequenced the whole genome of Streptococcus thermophilus MTCC 5461, the strain isolated from a curd source, by 454 GS-FLX titanium and Ion Torrent PGM. We performed comparative genome analysis using the local BLAST and RDP for 16S rDNA comparison and by the RAST server for functional comparison against the published genome sequence of Streptococcus thermophilus CNRZ 1066. The whole genome size of S. thermophilus MTCC 5461 is of 1.73Mb size with a GC content of 39.3%. Streptococcal virulence-related genes are either inactivated or absent in the strain. The genome possesses coding sequences for features important for a probiotic organism such as adhesion, acid tolerance, bacteriocin production, and lactose utilization, which was found to be conserved among the strains MTCC 5461 and CNRZ 1066. Biochemical analysis revealed the utilization of 17 sugars by the bacterium, where the presence of genes encoding enzymes involved in metabolism for 16 of these 17 sugars were confirmed in the genome. This study supports the facts that the strain MTCC 5461 is nonpathogenic and harbors essential features that can be exploited for its probiotic potential.

• Genomics & Informatics
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• v.10 no.4
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• pp.226-233
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• 2012

Since the advent of whole-genome sequencing, transposable elements (TEs), just thought to be 'junk' DNA, have been noticed because of their numerous copies in various eukaryotic genomes. Many studies about TEs have been conducted to discover their functions in their host genomes. Based on the results of those studies, it has been generally accepted that they have a function to cause genomic and genetic variations. However, their infinite functions are not fully elucidated. Through various mechanisms, including de novo TE insertions, TE insertion-mediated deletions, and recombination events, they manipulate their host genomes. In this review, we focus on Alu, L1, human endogenous retrovirus, and short interspersed element/variable number of tandem repeats/Alu (SVA) elements and discuss how they have affected primate genomes, especially the human and chimpanzee genomes, since their divergence.

• Asian-Australasian Journal of Animal Sciences
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• v.14 no.12
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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 Life Science
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• v.26 no.7
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• pp.855-867
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• 2016

The horse is relatively earlier domesticated animal species. Domesticated horses have been selected for their ability of racing, robustness, and disease-resistance. As a result, the thoroughbred horse genome has been condensed many genotypes related to exercise ability. In recent years, with the advent of NGS technologies, many studies were concentrated on finding superior genetic species in the horse genome in terms of genomics. Consequently, GWAS (Genome-wide Association study) is applied to horse genome, then genetic marker is revealed for superior racing ability. In addition, RNA-Seq is utilized as a method for analyze of whole transcript profiling in specific samples. By using this approach, specific gene expression patterns and transcript sequences can be revealed in various samples such as each individual, before and after exercise state, and each tissue. DNA methylation, a strong factor that regulate gene expression without the change of DNA sequence, have got a lot of attention. In horse genome, exercise- or individual-specific DNA methylation patterns were detected, and could be useful to develop selective marker of superior horses. MicroRNAs inhibit gene expression, and transposable elements accounted for half of the mammalian genome. These two elements are the crucial factors in functional genomics, and could be applied to the selection of superior horses. As the functional genomics and epigenomics advance, then these technologies introduced in this paper were applied to select superior horses. In this paper, the studies for selection of superior horses through genetic technologies, and development possibilities of these studies were discussed.

• Journal of Convergence for Information Technology
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• v.10 no.3
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• pp.76-91
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• 2020

Whole genome sequence of Abeliophyllum distichum Nakai (Oleaceae) cultivar Ok Hwang 1 Ho, which is Korean endemic species, was recently sequenced to understand its characteristics. Acteoside is one of major useful compounds presenting various activities, and its several proposed biochemical pathways were reviewed and integrated to make precise biochemical pathway. Utilizing MetaPre-AI^TM which was developed for predicting secondary metabolites based on whole genome with the precise biochemical pathway of acteoside and the InfoBoss Pathway Database, we successfully rescued all enzymes involved in this pathway from the genome sequences, presenting that A. distichum cultivar Ok Hwang 1 Ho may produce acteoside. High-performance liquid chromatography result displayed that callus of A. distichum cultivar Ok Hwang 1 Ho contained acteoside as well as isoacteoside which may be derived from acteoside. Taken together, we successfully showed that MetaPre-AI^TM can predict secondary metabolite from plant whole genomes. In addition, this method will be efficient to predict secondary metabolites of many plant species because DNA can be analyzed more stability than chemical compounds.

• Asian-Australasian Journal of Animal Sciences
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• v.31 no.1
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• pp.13-18
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• 2018

Objective: Meat quality including muscle color in chickens is an important trait and continuous selective pressures for fast growth and high yield have negatively impacted this trait. This study was conducted to investigate genetic variations responsible for regulating muscle color. Methods: Whole genome re-sequencing analysis using Illumina HiSeq paired end read method was performed with pooled DNA samples isolated from two broiler chicken lines divergently selected for muscle color (high muscle color [HMC] and low muscle color [LMC]) along with their random bred control line (RAN). Sequencing read data was aligned to the chicken reference genome sequence for Red Jungle Fowl (Galgal4) using reference based genome alignment with NGen program of the Lasergene software package. The potential causal single nucleotide polymorphisms (SNPs) showing non-synonymous changes in coding DNA sequence regions were chosen in each line. Bioinformatic analyses to interpret functions of genes retaining SNPs were performed using the ingenuity pathways analysis (IPA). Results: Millions of SNPs were identified and totally 2,884 SNPs (1,307 for HMC and 1,577 for LMC) showing >75% SNP rates could induce non-synonymous mutations in amino acid sequences. Of those, SNPs showing over 10 read depths yielded 15 more reliable SNPs including 1 for HMC and 14 for LMC. The IPA analyses suggested that meat color in chickens appeared to be associated with chromosomal DNA stability, the functions of ubiquitylation (UBC) and quality and quantity of various subtypes of collagens. Conclusion: In this study, various potential genetic markers showing amino acid changes were identified in differential meat color lines, that can be used for further animal selection strategy.