• 한국생물공학회:학술대회논문집
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• 2000.11a
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• pp.660-664
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• 2000

To clone genes related UK-58,852 production, genomic DNA of strain Actinodura roseorufa was used for the construction of genomic library using pOJ446 cosmid vector. The genomic library was screened rising dehydratase PCR product and eryA gene as a DNA hybridization probe. pHD54 was isolated, which contained an approximately 35kb of inserted DNA. BamHI, SmaI and sonicater fragments hybridized to eryA probe. All of pHD54 BgmHI, SmaI and sonicater fragments were subcloned into pGEM7 and some fragments which hybridized to eryA probe were sequenced. The nucleotide sequence was analysed using BLAST program. The sequence identities were observed in KS,AT, KR, ER and PKS loading domains. Also oxidoreductase showed similarity to rifamycin module10, and dTDP-D-glucose 4,6 dehydratase and TDP-D-glucose synthase involved in biosynthesis of sugar showed similarity to Streptomyces argillaceus.

• Journal of Microbiology and Biotechnology
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• v.7 no.2
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• pp.157-159
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• 1997

A 340-bp chitin synthase gene(CHS) fragment was cloned from the genomic DNA of Pyricularia oryzae using a PCR process with two primer DNAs corresponding to highly conserved sequences within fungal CHS genes. The entire DNA nucleotide sequences of the cloned DNA fragment were determined and analyzed. The amino acid sequences deduced from the nucleotide sequence of the amplified DNA fragment showed 86% homology to that of the Aspergillus fumigatus CHSE gene (9). Using this PCR-amplified DNA, about 2.3 kb of including the PCR fragment of CHSE gene was cloned from genomic library.

• Mycobiology
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• v.46 no.4
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• pp.361-369
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• 2018

The rice blast fungus, Magnaporthe oryzae, is an important pathogen of rice plants. It is well known that genes encoded in the genome have different evolutionary histories that are related to their functions. Phylostratigraphy is a method that correlates the evolutionary origin of genes with evolutionary transitions. Here we applied phylostratigraphy to partition total gene content of M. oryzae into distinct classes (phylostrata), which we designated PS1 to PS7, based on estimation of their emergence time. Genes in individual phylostrata did not show significant biases in their global distribution among seven chromosomes, but at the local level, clustering of genes belonging to the same phylostratum was observed. Our phylostrata-wide analysis of genes revealed that genes in the same phylostratum tend to be similar in many physical and functional characteristics such as gene length and structure, GC contents, codon adaptation index, and level of transcription, which correlates with biological functions in evolutionary context. We also found that a significant proportion of genes in the genome are orphans, for which no orthologs can be detected in the database. Among them, we narrowed down to seven orphan genes having transcriptional and translational evidences, and showed that one of them is implicated in asexual reproduction and virulence, suggesting ongoing evolution in this fungus through lineage-specific genes. Our results provide genomic basis for linking functions of pathogenicity factors and gene emergence time.

• Parasites, Hosts and Diseases
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• v.47 no.2
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• pp.103-107
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• 2009

The genus Acanthamoeba can cause severe infections such as granulomatous amebic encephalitis and amebic keratitis in humans. However, little genomic information of Acanthamoeba has been reported. Here, we constructed Acanthamoeba expressed sequence tags (EST) database (Acanthamoeba EST DB) derived from our 4 kinds of Acanthamoeba cDNA library. The Acanthamoeba EST DB contains 3,897 EST generated from amebae under various conditions of long term in vitro culture, mouse brain passage, or encystation, and downloaded data of Acanthamoeba from National Center for Biotechnology Information (NCBI) and Taxonomically Broad EST Database (TBestDB). The almost reported eDNA/genomic sequences of Acanthamoeba provide stand alone BLAST system with nucleotide (BLAST NT) and amino acid (BLAST AA) sequence database. In BLAST results, each gene links for the significant information including sequence data, gene orthology annotations, relevant references, and a BlastX result. This is the first attempt for construction of Acanthamoeba database with genes expressed in diverse conditions. These data were integrated into a database (http://www. amoeba.or.kr).

• BMB Reports
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• v.39 no.4
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• pp.464-467
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• 2006

Recently, the nucleotide sequences of entire genomes became available. This information combined with older sequencing data discloses the exact chromosomal location of millions of nucleotide markers stored in the databases at NCBI, EMBO or DDBJ. Despite having resolved the intron/exon structures of all described genes within these genomes with a stroke of a pen, the sequencing data opens up other interesting possibilities. For example, the genomic mapping of the end sequences of the human, murine and rat BAC libraries generated at The Institute for Genomic Research (TIGR), reveals now the entire encompassed sequence of the inserts for more than a million of these clones. Since these clones are individually stored, they are now an invaluable source for experiments which depend on genomic DNA. Isolation of smaller fragments from such clones with standard methods is a time consuming process. We describe here a reliable one-step cloning technique to obtain a DNA fragment with a defined size and sequence from larger genomic clones in less than 48 hours using a standard vector with a multiple cloning site, and common restriction enzymes and equipment. The only prerequisites are the sequences of ends of the insert and of the underlying genome.

• International Journal of Industrial Entomology and Biomaterials
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• v.15 no.2
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• pp.123-130
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• 2007

The Hsp 20.8 and Hsp 90 cDNA sequence retrieved from NCBI database and consists of 764 bp and 2582 bp lengths respectively. The corresponding cDNA homologus sequences were BLAST searched in Bombyx mori genomic DNA database and two genomic contigs viz., BAAB01120347 and AADK01011786 showed maximum homology. In B. mori Hsp 20.8 and Hsp 90 is encoded by single gene without intron. Specific primers were used to amplify the Hsp 20.8 gene and Hsp 90 variable region from genomic DNA by using the PCR. Obtained products were 216 bp in Hsp 20.8 and 437 bp in Hsp 90. There was no variation found in the six silkworm races PCR products size of contrasting response to thermal tolerance. The comparison of the sequenced nucleotide variations through multiple sequence alignment analysis of Hsp 90 variable region products of three races not showed any differences respect to their thermotolerance and formed the clusters among the voltinism. The comparison of aminoacid sequences of B. mori Hsps with dipteran and other insect taxa revealed high percentage of identity growing with phylogenetic relatedness of species. The conserved domains of B. mori Hsps predicted, in which the Hsp 20.8 possesses ${\alpha}-crystallin$ domain and Hsp 90 holds HATPase and Hsp 90 domains.

• Korean Journal of Microbiology
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• v.38 no.4
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• pp.267-275
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• 2002

We have developed GComp as an analysis tool for microbial genome comparison. This tool exploits BLAST or FASTA as a preprocessing program for local alignments to detect homologous regions, parses the homology search results, and generates tables and files to show homology relationship between two genomes at a glance. The interface for graphical representation of the comparative genomic analysis has been also implemented. Our test cases shows that the program can be useful in practice for intuitive and quantitative comparison of microbial genome sequence pairs as well as self-genome analysis. A few additional features have been devised and designed, which will be added in the further development.

• Proceedings of the Microbiological Society of Korea Conference
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• 2002.10a
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• pp.185-193
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• 2002

We have developed GComp as an analysis tool for comparative analysis of microbial genomes. Thetool uses BLAST or FASTA as a preprocessing program for local alignments, parses the homology search results, and generates tables and files to show homology relationship between two genomes at a glance. The interface for graphical representation of the comparative genomic analysis has been also implemented. Through analysis of a few pairs of microbial genome sequences, the program has been proved to be practically useful and a few additional features have been devised and designed, which will be added in the further development.

• Journal of Life Science
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• v.11 no.1
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• pp.39-41
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• 2001

Cytohesin family has been thought to participate in inside-outside signaling linking growth factor receptor stimulation of PI 3-kinase to cell adhesion and stimulate nucleotide exchange of ARF through its Sec7 domain. The genomic structure of the cytohesin family was analyzed by BLAST search using cDNA and genomic DNA sequences from the GeneBank database. The cytohesin-2 was encoded by 12 exons. while the cytohesin-4 was encoded by 13 exons. The Sec7 and PH domains were not encoded by separate exons. In an analysis of retroviral integration, those two families did not contain any retroviral elements in introns or exons. The phylogenetic tree calculated by the neighbor-joining method suggests that the cytohesin-1 family was closely related to cytohesin-3 (ARNO3) family. These date could be of great use in further studies for resolving the exact function and evolution of the cytohesin family.

• Korean Journal of Agricultural Science
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• v.36 no.2
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• pp.159-165
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• 2009

This study was conducted to identify the PERV (Porcine Endogenous Retrovirus) integration sites and their characterizations using the porcine genomic sequence information. Total 114 Mb (4.2%) sequence of the 2.7 Gb pig genome was investigated for the PERV sequences. As the results, 8 PERV sequences were identified and their genomic structures were deduced from the BLAST searches against previously known PERV genes. Seven PERVs have internal deletions in the protein coding region and they will not be functional. The other one also has internal deletions in the gag and env genes, indicating this PERV is also defective. Even though we could not identify the functional PERVs in this study, the results presented here can be used for the fundamental research materials for controlling PERV infections in relation to xenotransplantation using porcine organs and tissues.