• Genomics & Informatics
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• 제10권1호
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• pp.1-8
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• 2012

Recently, the technologies of DNA sequence variation and gene expression profiling have been used widely as approaches in the expertise of genome biology and genetics. The application to genome study has been particularly developed with the introduction of the nextgeneration DNA sequencer (NGS) Roche/454 and Illumina/ Solexa systems, along with bioinformation analysis technologies of whole-genome $de$ $novo$ assembly, expression profiling, DNA variation discovery, and genotyping. Both massive whole-genome shotgun paired-end sequencing and mate paired-end sequencing data are important steps for constructing $de$ $novo$ assembly of novel genome sequencing data. It is necessary to have DNA sequence information from a multiplatform NGS with at least $2{\times}$ and $30{\times}$ depth sequence of genome coverage using Roche/454 and Illumina/Solexa, respectively, for effective an way of de novo assembly. Massive shortlength reading data from the Illumina/Solexa system is enough to discover DNA variation, resulting in reducing the cost of DNA sequencing. Whole-genome expression profile data are useful to approach genome system biology with quantification of expressed RNAs from a wholegenome transcriptome, depending on the tissue samples. The hybrid mRNA sequences from Rohce/454 and Illumina/Solexa are more powerful to find novel genes through $de$ $novo$ assembly in any whole-genome sequenced species. The $20{\times}$ and $50{\times}$ coverage of the estimated transcriptome sequences using Roche/454 and Illumina/Solexa, respectively, is effective to create novel expressed reference sequences. However, only an average $30{\times}$ coverage of a transcriptome with short read sequences of Illumina/Solexa is enough to check expression quantification, compared to the reference expressed sequence tag sequence.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2002년도 제1차워크샵
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• pp.105-121
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• 2002

최근 인간 지놈(genome)의 DNA가 밝혀져서 많은 관심을 받았는데, 이를 수행하는 방법을 소개한다. Human Genome Project에서 채택한 BAC-to-BAC 방식과 Celera 회사에서 채택한 whole genome shotgun 방식을 설명한다. 또한 두 방식에서 공히 fragment assembly 프로그램을 사용하는데, 이 프로그램의 개요를 설명한다.

• 한국식품과학회지
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• 제48권2호
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• pp.128-132
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• 2016

PEG를 이용하여 WGA 수행 시 DNA 증폭 효율을 높이고 이를 식중독 세균의 DNA 증폭 및 검출에 적용하고자 하였다. 등온 증폭 반응인 WGA에 여러 종류의 PEG를 첨가하여 증폭한 결과, 1.5% 농도의 PEG 4,000을 첨가하는 것이 가장 효율이 높음을 알 수 있었다. 증폭 정도를 정량적으로 파악하기 위하여 3종의 식중독 세균 DNA를 이용하여 WGA를 수행하였으며 real-time PCR로 정량분석하였다. S. Typhimurium, L. monocytogenes, V. parahaemolyticus의 경우에 WGA를 하지 않은 DNA에 비하여 각각 7,777.01배, 9,981.22배, 1,239.03배 정도로 DNA의 양이 증폭되는 것을 확인하였다. 또한 PEG를 첨가함으로써 18배에서 40배의 핵산 증폭 효과가 더 있음을 알 수 있었다. 따라서 식품에 미량의 농도로 존재하는 식중독 세균은 PEG가 첨가된 WGA 반응을 통하여 검출 가능성을 높일 수 있음을 알 수 있었다.

• Genomics & Informatics
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• 제19권2호
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• pp.19.1-19.9
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• 2021

Plant height is an important component of plant architecture and significantly affects crop breeding practices and yield. We studied DNA variations derived from F5 recombinant inbred lines (RILs) with 96.8% homozygous genotypes. Here, we report DNA variations between the normal and dwarf members of four lines harvested from a single seed parent in an F6 RIL population derived from a cross between Glycine max var. Peking and Glycine soja IT182936. Whole genome sequencing was carried out, and the DNA variations in the whole genome were compared between the normal and dwarf samples. We found a large number of DNA variations in both the dwarf and semi-dwarf lines, with one single nucleotide polymorphism (SNP) per at least 3.68 kb in the dwarf lines and 1 SNP per 11.13 kb of the whole genome. This value is 2.18 times higher than the expected DNA variation in the F6 population. A total of 186 SNPs and 241 SNPs were discovered in the coding regions of the dwarf lines 1282 and 1303, respectively, and we discovered 33 homogeneous nonsynonymous SNPs that occurred at the same loci in each set of dwarf and normal soybean. Of them, five SNPs were in the same positions between lines 1282 and 1303. Our results provide important information for improving our understanding of the genetics of soybean plant height and crop breeding. These polymorphisms could be useful genetic resources for plant breeders, geneticists, and biologists for future molecular biology and breeding projects.

• Biotechnology and Bioprocess Engineering:BBE
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• 제5권3호
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• pp.159-163
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• 2000

The genome sequencing project has generated and will contitute to generate enormous amounts of sequence data. Since the first complete genome sequence of bacterium Haemophilus in fluenzae was published in 1995, the complete genome sequences of 2 eukaryotic and about 22 prokaryotic organisms have detemined. Given this everincreasing amounts of sequence information, new strategies are necessary to efficiently pursue the phase of the geome project- the elucidation of gene expression patterns and gene product function on a whole genome scale. In order to assign functional information to the genome sequence, DNA chip technology was developed to efficienfly identify the differential expression pattern of indepondent biogical samples. DNA chip provides a new tool for genome expreesion analysis that may revolutionize revolutionize many aspects of human kife including mew surg discovery and human disease diagnostics.

• 한국생물공학회:학술대회논문집
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• 한국생물공학회 2003년도 생물공학의 동향(XIII)
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• pp.815-820
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• 2003

A huge database resulted from whole genome sequencing has provided a possibility of new information that is likely to extent the scope and thus changes the way of approach for the functional assigning of putative open reading frames annotated by whole genome sequence analyses. These are mainly realized by ease, one-step identification of putative genes using genomics or proteomics tools. A major challenge remained in biotechnology may translate these informations into better ways to screen or select a gene as a representative sequence. Further attempts to mine the related whole genes or partial DNA fragment from whole genome treasure, and then the incorporation of these sequences into a representative template, will result in the use of putative genes that can be translated into functional proteins or allowed the generation of new lineages as a valuable pool. Such screens enable rapid biochemical analysis and easy isolation of the target activity, thereby accelerating the screening of novel enzymes from the expanded library with related sequences. Information-based PCR amplification of whole genes and reconstitution of functional DNA fragments will provide a platform for expanding the functional spaces of potential enzymes, especially when used mixed- or metagenome as gene resources.

• Journal of Microbiology and Biotechnology
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• 제22권5호
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• pp.649-653
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• 2012

A temperate phage was isolated from emetic Bacillus cereus NCTC 11143 by mitomycin C and characterized by transmission electron microscopy and DNA and protein analyses. Whole genome sequencing of Bacillus phage 11143 was performed by GS-FLX. The phage has a dsDNA genome of 39,077 bp and a 35% G+C content. Bioinformatic analysis of the phage genome revealed 49 putative ORFs involved in replication, morphogenesis, DNA packaging, lysogeny, and host lysis. Bacillus phage 11143 could be classified as a member of the Siphoviridae family by morphology and genome structure. Genomic comparisons at the DNA and protein levels revealed homologous genetic modules with patterns and morphogenesis proteins similar to those of other Bacillus phages. Thus, Bacillus phages might have a mosaic genetic relationship.

• Journal of Dairy Science and Biotechnology
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• 제42권1호
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• pp.18-22
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• 2024

In this study, we performed whole-genome sequencing of Levilactobacillus brevis KL251 (KL251) isolated from kimchi. The KL251 genome, characterized by a circular chromosome spanning 2,345,062 base pairs with a GC content of 45.78%, was analyzed. KL251 contains 2,275 coding DNA sequences (CDSs), 56 transfer RNAs (tRNAs), and 4 ribosomal RNAs (rRNAs). Genes associated with gamma-aminobutyric acid (GABA) production and CRISPR-Cas systems were identified and could potentially be used for GABA synthesis and defense against foreign DNA. Additionally, the presence of functional genes involved in isoprenoid biosynthesis, glutathione generation, and redox sensing showed that cellular metabolism and stress responses were important characteristics of this genome. These genomic findings suggest that the KL251 strain could potentially have several applications, including food fermentation, probiotics, dairy product starters, and the development of health-enhancing products.

• Genomics & Informatics
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• 제14권3호
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• pp.90-95
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• 2016

Nuclear mitochondrial DNA segment (Numt) insertion describes a well-known phenomenon of mitochondrial DNA transfer into a eukaryotic nuclear genome. However, it has not been well understood, especially in plants. Numt insertion patterns vary from species to species in different kingdoms. In this study, the patterns were surveyed in nine plant species, and we found some tip-offs. First, when the mitochondrial genome size is relatively large, the portion of the longer Numt is also larger than the short one. Second, the whole genome duplication event increases the ratio of the shorter Numt portion in the size distribution. Third, Numt insertions are enriched in exon regions. This analysis may be helpful for understanding plant evolution.

• 한국미생물·생명공학회지
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• 제51권4호
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• pp.566-568
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• 2023

In this report, we present the whole-genome sequence of Bifidobacterium bifidum DS0908 isolated from the human fecal sample. The genome composed of a single circular chromosome is 2,223,317 bp long and the DNA G+C content is 62.65%. No virulence genes were detected in the genomic sequences of B. bifidum DS0908.