• Microbiology and Biotechnology Letters
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• v.51 no.3
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• pp.289-292
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• 2023

Thermotolerant Bacillus subtilis NIB353 was isolated from Nuruk, a traditional Korean fermentation starter. The complete B. subtilis NIB353 genome sequence was obtained using MinION and Illumina (MiSeq) platforms. The B. subtilis NIB353 genome sequence was 4,247,447 bp with a GC content of 43%. The B. subtilis NIB353 strain exhibited orthologous average nucleotide identity values of 98.39% and 98.38% with B. subtilis 168 and B. subtilis ATCC6051a, respectively. The genome has been deposited in GenBank under the accession number NZ_CP089148.1.

• Microbiology and Biotechnology Letters
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• v.46 no.3
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• pp.300-312
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• 2018

Whole-genome sequencing of the wood-rotting fungus, Flammulina fennae, was carried out to identify carbohydrate-active enzymes (CAZymes). De novo genome assembly (31 kmer) of short reads by next-generation sequencing revealed a total genome length of 32,423,623 base pairs (39% GC). A total of 11,591 gene models in the assembled genome sequence of F. fennae were predicted by ab initio gene prediction using the AUGUSTUS tool. In a genome-wide comparison, 6,715 orthologous groups shared at least one gene with F. fennae and 10,667 (92%) of 11,591 genes for F. fennae proteins had orthologs among the Dikarya. Additionally, F. fennae contained 23 species-specific genes, of which 16 were paralogous. CAZyme identification and annotation revealed 513 CAZymes, including 82 auxiliary activities, 220 glycoside hydrolases, 85 glycosyltransferases, 20 polysaccharide lyases, 57 carbohydrate esterases, and 45 carbohydrate binding-modules in the F. fennae genome. The genome information of F. fennae increases the understanding of this basidiomycete fungus. CAZyme gene information will be useful for detailed studies of lignocellulosic biomass degradation for biotechnological and industrial applications.

• Proceedings of the Korean Society of Life Science Conference
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• 2003.10a
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• pp.14-27
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• 2003

The genomes of Arabidopsis and rice have been fully sequenced. Genomic sequencing provides global information about genome structure and organization. A comprehensive research account of our recent studies conducted on genome painting, comparative genomics and genome fusion is provided in order to project the prospects of plant cytogenetic research in post-genomics era. Genome analysis by GISH using genome painting is demonstrated as an excellent means suitable for visualization of a whole genome, since total genomic DNA representing the overall molecular composition of the genome is used as a probe. FISH on extended DNA fibers has been developed for high-resolution FISH and has contributed to determining the copy number and order of genes. We have also mapped a number of genes involving starch synthesis on wheat chromosomes by FISH and compared the position of these genes on linkage map of rice. Macro synteny between wheat and rice can be observed by comparing the location of these genes in spite of the fact that the size of DNA per chromosome differs by 20 fold in two. Moreover, to approach our goal towards making bread and udon noodles from rice flour in future by incorporating bread making and the noodle qualifies in rice, we have been successful in introducing large genomic DNA fragments containing agronomically important genes of wheat into a rice by successive introduction of large insert BAC clones, there by expanding genetic variability in rice. We call this method genome fusion.

• Journal of Animal Science and Technology
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• v.64 no.1
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• pp.183-186
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• 2022

Lactiplantibacillus plantarum (L. plantarum) ST was isolated from De'ang pickled tea in Yunnan Province, China. The genomes of strain ST were fully sequenced and analyzed using the PacBio RS II sequencing system. Our previous study has shown that L. plantarum ST is a potential probiotic strain. It had strong tolerance in the simulated artificial gastrointestinal tract, and in the antagonism tests, this strain showed strong antibacterial activity. Therefore, as a probiotic, it may be used in animal breeding. L. plantarum ST genome was composed of 1 circular chromosome and 7 plasmids. The length of the whole genome was 3320817 bp, and the annular chromosome size was 3058984 bp, guanine + cytosine (G ± C) content (%) was 44.76%, which contained 2945 protein-coding sequences (CDS). This study will contribute to a further comprehensive understanding of L. Plantarum ST at the genomic level and provide a theoretical basis for its future application in animal breeding.

• Proceedings of the Korea Information Processing Society Conference
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• 2007.11a
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• pp.272-273
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• 2007

현대 유전체학 기술의 진보는 생물학적으로 중요한 의미를 갖는 생물들의 유전체 서열의 규명 genome sequencing)에 힘입은 바 크다. 기존의 유전체 서열결정법은 주로 염기변이율이 낮은 생물들에 초점을 맞추어 왔다. 하지만 염기변이율이 높은 생물들의 유전체 염기서열을 결정할 필요가 높아짐에 따라 이를 위한 방법론에 대한 연구가 활발히 진행되고 있다. 염기변이율이 높은 생물들의 이배체 (diploid) 유전체 서열이 효과적으로 결정될 수 있을 경우 기존의 유전체 서열비교의 방법론에도 변화가 요청되고 있는 실정이다. 기존의 유전체 서열비교 (whole-genome alignment) 방법론은 반수체 (haploid) 유전체들의 서열비교을 위해 개발되었지만, 염기변이율이 높은 생물들의 유전체 서열비교에는 반수체 유전체들 비교에 특화된 도구들이 필요하다. 또한 현재 서열비교를 시각화하는 소프트웨어들도 반수체 유전체 비교를 위해 개발된 실정이다. 본 논문의 목표는 이배체 유전체 서열을 비교하는 방법론을 개발을 용이하기위해 이배체 유전체의 서열을 생성하는 도구를 개발하는 것이다. 개발된 도구는 실제 일어날 수 있는 염기변이와 genomic rearrangement를 사용자의 입력을 받아 다수의 생물들의 유전체 서열을 생성해 낸다. 이를 통해 이배체 유전체 서열을 비교하는 도구의 개발을 용이하게 하는데 초첨을 맞추고 있다.

• Genomics & Informatics
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• v.11 no.1
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• pp.38-45
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• 2013

In cancer genome studies, the annotation of newly detected oncogene/tumor suppressor gene candidates is a challenging process. We propose using concept lattice analysis for the annotation and interpretation of genes having candidate somatic mutations in whole-exome sequencing in acute myeloid leukemia (AML). We selected 45 highly mutated genes with whole-exome sequencing in 10 normal matched samples of the AML-M2 subtype. To evaluate these genes, we performed concept lattice analysis and annotated these genes with existing knowledge databases.

• Molecules and Cells
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• v.38 no.5
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• pp.466-473
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• 2015

Over the last 30 years, Hanwoo has been selectively bred to improve economically important traits. Hanwoo is currently the representative Korean native beef cattle breed, and it is believed that it shared an ancestor with a Chinese breed, Yanbian cattle, until the last century. However, these two breeds have experienced different selection pressures during recent decades. Here, we whole-genome sequenced 10 animals each of Hanwoo and Yanbian cattle (20 total) using the Illumina HiSeq 2000 sequencer. A total of approximately 3.12 and 3.07 billion sequence reads were mapped to the bovine reference sequence assembly (UMD 3.1) at an average of approximately 10.71- and 10.53-fold coverage for Hanwoo and Yanbian cattle, respectively. A total of 17,936,399 single nucleotide polymorphisms (SNPs) were yielded, of which 22.3% were found to be novel. By annotating the SNPs, we further retrieved numerous nonsynonymous SNPs that may be associated with traits of interest in cattle. Furthermore, we performed whole-genome screening to detect signatures of selection throughout the genome. We located several promising selective sweeps that are potentially responsible for economically important traits in cattle; the PPP1R12A gene is an example of a gene that potentially affects intramuscular fat content. These discoveries provide valuable genomic information regarding potential genomic markers that could predict traits of interest for breeding programs of these cattle breeds.

• Korean journal of applied entomology
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• v.61 no.3
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• pp.449-460
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• 2022

The morphology and whole genome sequence of Spodoptera exigua nucleopolyhedrovirus K1 (SeNPV-K1) isolated in Korea were analyzed for the use as an eco-friendly control source against S. exigua. The polyhedra of SeNPV-K1 was amorphous with a size of 0.6-1.8 ㎛, and there was no external difference with the previously reported SeNPV. As a result of analyzing the nucleotide sequence of the whole genome, it was composed of 135,756 bp, which is 145 bp more than that of the previously reported SeNPV. The G+CG+C content was 44% and there were 6 homologous repeated sequences, so there was no significant difference from the previous report. As a result of ORF analysis, SeNPV-K1 had 137, two fewer than those previously reported, and 4 ORFs present only in SeNPV-K1 were confirmed. These 4 ORFs are non-essential genes and were not considered to have a significant influence on the characteristics of the SeNPV. The genome vista analysis showed that the overall sequence similarity between SeNPV-K1 and the previously reported SeNPV was very high. The whole genome of SeNPV-K1 analyzed for the first time in Korea was found to be similar to the previously reported SeNPV, but it was confirmed that it was a novel resource in Korea with different isolate.

• Korean Journal of Organic Agriculture
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• v.31 no.4
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• pp.395-412
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• 2023

The morphology and whole genome sequence of Hyphantria cunea nucleopolyhedrovirus W1 (HycuNPV-W1) isolated in Korea were analyzed for the use as an eco-friendly control agent against H. cunea. The HycuNPV-W1 had irregular tetrahedral polyhedra with a size of 1.5-2.2 ㎛ which is similar to that of previously reported HycuNPV isolated in Korea. As a result of whole viral genome analysis, HycuNPV-W1 was composed of 131,353 bp, which is 1,606 bp shorter than that of the previously reported HycuNPV. The G+C content was 45% and six of the homologous repeated regions were found, so there was no significant difference from the previous report. As a result of ORF analysis, HycuNPV-W1 contains total of 145 ORFs which is three ORFs less than the previous report, while two ORFs were exclusively found in HycuNPV-W1. The functions of these ORFs remains unclear and are not considered to have a significant influence on the characteristics of the HycuNPV. The genome vista analysis showed that the overall sequence identity between HycuNPV-W1 and the previously reported HycuNPV was very high. The whole genome of HycuNPV-W1 analyzed was found to be similar to those of the previously reported HycuNPV, however, it is supposed to be a novel resource in Korea with different isolate.

• 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.