• Journal of Plant Biotechnology
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• v.36 no.2
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• pp.130-136
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• 2009

Rice (Oryza sativa) is the most important staple crop in Korea. With its small genome size of 389Mb, rice is a model plant for genome research. We analyzed expressed sequence tag (EST) clones from immature seeds of rice (cv. Ilpum) at 20 days after heading. The 25,668 EST clones were clustered by using SeqMan program and 7,509 clones were selected as unique clones. We compared the 7,509 unique genes with KOME database including the 32,127 FL-cDNA in rice. Finally, 4,990 clones were homologous and 2,519 clones non-homologous to FL-cDNA clones. In addition, we mapped the 7,509 cDNA clones by using TIGR rice pseudomolecule version 5. Ultimately, 7,347 clones were matched to be significant clones related to the TIGR rice pseudomolecules, but 162 clones were unmapped. For the clustering of orthologous group genes, we further analyzed the 7,509 EST clones from immature seeds using NCBI clusters of orthologous groups database. Among the clones, 4,968 clones were categorized into information storage and processing, cellular processes and signaling, metabolism and poorly characterized genes, proportioning 799 (14.89%), 1,536 (28.3%), 1,148 (21.2%) and 1,936 (35.7%) clones to the previous four categories, respectively.

• Journal of Plant Biotechnology
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• v.36 no.3
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• pp.281-288
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• 2009

Seed germination is the important stage to express many genes for regulation of energy metabolism, starch degradation and cell division from seed dormancy state. For the functional analysis of seed germination mechanisms, we were analyzed the rice cDNA clones (Oryzasativa cultivar Ilpum) obtained from seed imbibition during 48 hours. Total number of 18,101 Expressed Sequence Tags (ESTs) were clustered using SeqMan program. Among them, 8,836 clones were identified as unique clones. We identified the chitinase gene specifically expressed in seed germination and amylase gene involved to starch degradation from the full length cDNA analysis, and several genes were registered to NCBI GeneBank. To analyzed the commonly expressed genes between inmature seed and germinated seed, 25,66 inmature ESTs and 18,101 germinated ESTs were clustered using SeqMan program and identified 2,514 clones as commonly expressed unigene. Among them, alpha-glubulin and alcohol dehydrogenase I were supposed to LEA genes only expressed in the immature and germinated seed stages. For the clustering of orthologous group genes, we further analyzed the 8,836 EST clones from germinating seeds using NCBI clusters of orthologous groups database. Among the clones, 5,076 clones were categorized into information storage and processing, cellular processes and signaling, metabolism and poorly characterized genes, proportioning 783 (14.29%), 1,484 (27%), 1,363 (24.8%) and 1,869 (34%) clones to the previous four categories, respectively.

• Journal of Life Science
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• v.31 no.2
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• pp.219-222
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• 2021

In this study, we examined low molecular weight peptides using proteomics in order to identify their original proteins, derive their peptides, and determine the functions of the proteins in Tenebrio molitor, the mealworm (larvae, pupae, or adult) from which the peptides were extracted. Fifty-four proteins were finally identified through an analysis of proteome to derive the analyzed peptides. The proteins that induced low molecular weight peptides were identified to be the most abundant in adults only, and the next highest were derived from a group containing both adults and larva. However, other groups, including pupa, were detected to have a lower frequency of peptides. As a result of orthologous classification of the detected proteins, the general function prediction was only investigated at the highest frequency among the examined proteins. Proteins related to chromatin structure and dynamics were detected by their higher frequency among functional classes. The next highest frequency was shown by proteins related to amino acid transport and metabolism and carbohydrate transport and metabolism. Therefore, it is assumed that proteins correlated with chromatin, amino acid, and carbohydrate metabolisms are easily induced into low molecular weight peptides, and that their peptides could play a role as bioactive substances.

• Parasites, Hosts and Diseases
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• v.49 no.4
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• pp.341-347
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• 2011

Acanthamoeba infection is difficult to treat because of the resistance property of Acanthamoeba cyst against the host immune system, diverse antibiotics, and therapeutic agents. To identify encystation mediating factors of Acanthamoeba, we compared the transcription profile between cysts and trophozoites using microarray analysis. The DNA chip was composed of 12,544 genes based on expressed sequence tag (EST) from an Acanthamoeba ESTs database (DB) constructed in our laboratory, genetic information of Acanthamoeba from TBest DB, and all of Acanthamoeba related genes registered in the NCBI. Microarray analysis indicated that 701 genes showed higher expression than 2 folds in cysts than in trophozoites, and 859 genes were less expressed in cysts than in trophozoites. The results of real-time PCR analysis of randomly selected 9 genes of which expression was increased during cyst formation were coincided well with the microarray results. Eukaryotic orthologous groups (KOG) analysis showed an increment in T article (signal transduction mechanisms) and O article (posttranslational modification, protein turnover, and chaperones) whereas significant decrement of C article (energy production and conversion) during cyst formation. Especially, cystein proteinases showed high expression changes (282 folds) with significant increases in real-time PCR, suggesting a pivotal role of this proteinase in the cyst formation of Acanthamoeba. The present study provides important clues for the identification and characterization of encystation mediating factors of Acanthamoeba.

• KSBB Journal
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• v.18 no.1
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• pp.39-44
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• 2003

A Gene content phylogenetic tree and a 16s rRNA based phylogenetic tree were compared for 33 whole-genome sequenced procaryotes, neighbor joining and bootstrap methods (n=1,000). Ratio of conserved COG (clusters of orthologous groups of proteins) to orthologs revealed that they were within the range of 4.60% (Mezorhizobium loti) or 56.57% (Mycopiasma genitalium). This meant that the ratio was diverse among analyzed procaryotes and indicated the possibility of searching for useful genes. Over 20% of orthologs were independent among the same species. The gene content tree and the 16s rDNA tree showed coincidence and discordance in Archaeabacteria, Proteobacteria and Firmicutes. This might have resulted from non-conservative genes in the gene content phylogenetic tree and horizontal gene transfer. The COG based gene content tree could be regarded as a midway phylogeny based on biochemical tests and nucleotide sequences.

• Genomics & Informatics
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• v.17 no.1
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• pp.5.1-5.9
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• 2019

The chinstrap (Pygoscelis antarcticus) and gentoo (P. papua) penguins are distributed throughout Antarctica and the sub-Antarctic islands. In this study, high-quality de novo assemblies of blood transcriptomes from these penguins were generated using the Illumina MiSeq platform. A total of 22.2 and 21.8 raw reads were obtained from chinstrap and gentoo penguins, respectively. These reads were assembled using the Oases assembly platform and resulted in 26,036 and 21,854 contigs with N50 values of 929 and 933 base pairs, respectively. Functional gene annotations through pathway analyses of the Gene Ontology, EuKaryotic Orthologous Groups, and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases were performed for each blood transcriptome, resulting in a similar compositional order between the two transcriptomes. Ortholog comparisons with previously published transcriptomes from the $Ad{\acute{e}}lie$ (P. adeliae) and emperor (Aptenodytes forsteri) penguins revealed that a high proportion of the four penguins' transcriptomes had significant sequence homology. Because blood and tissues of penguins have been used to monitor pollution in Antarctica, immune parameters in blood could be important indicators for understanding the health status of penguins and other Antarctic animals. In the blood transcriptomes, KEGG analyses detected many essential genes involved in the major innate immunity pathways, which are key metabolic pathways for maintaining homeostasis against exogenous infections or toxins. Blood transcriptome studies such as this may be useful for checking the immune and health status of penguins without sacrifice.

• Journal of Animal Science and Technology
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• v.66 no.2
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• pp.438-441
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• 2024

The Enterococcus faecium (E. faecium) strain AK_C_05 was isolated from cheonggukjang, the Korean traditional food, collected from a local market in South Korea. In this report, we presented the complete genome sequence of E. faecium strain AK_C_05. The genome of E. faecium strain AK_C_05 genome consisted of one circular chromosome (2,691,319 bp) with a guanine + cytosine (GC) content of 38.3% and one circular plasmid (177,732 bp) with a GC content of 35.48%. The Annotation results revealed 2,827 protein-coding sequences (CDSs), 18 rRNAs, and 68 tRNA genes. It possesses genes, which encodes enzymes such as alpha-galactosidase (EC 3.2.1.22), beta-glucosidase (EC 3.2.1.21) and alpha-L-arabinofuranosidase (EC 3.2.1.55) enabling efficient utilization of carbohydrates. Based on Clusters of Orthologous Groups analysis, E. faecium strain AK_C_05 showed specialization in carbohydrate transport and metabolism indicating the ability to generate energy using a variety of carbohydrates.

• Journal of Life Science
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• v.15 no.2 s.69
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• pp.261-266
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• 2005

To figure out conserved genes in 66 microbial species and measuring the degree of conservation, analyses based on COG (Clusters of Orthologous Groups of proteins) algorithm were applied. Sixty-six microbial genomes, including three eukaryotes, hold 63 conserved orthologs in common. The majority $(82.5\%)$ of the conserved genes was related to translation, meaning the importance of protein in living creatures. Ribosomal protein S12 (COG0048) and L14 (COG0093) were more conserved genes than others from the distance value analysis. Phylogenetically related microbes grouped in genome analysis by average and standard deviation of 63 conserved genes. The 63 conserved genes, found in this research, would be useful in basic research and applied ones such as antibiotic development.

• Asian-Australasian Journal of Animal Sciences
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• v.30 no.9
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• pp.1215-1224
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• 2017

Objective: To assess the differences in ovarian transcriptomes in Shan Ma ducks between their peak and late stages of egg production, and to obtain new transcriptomic data of these egg-producing ducks. Methods: The Illumina HiSeq 2000 system was used for high throughput sequencing of ovarian transcriptomes from Shan Ma ducks at their peak or late stages of egg production. Results: Greater than 93% of the sequencing data had a base quality score (Q score) that was not less than 20 (Q20). From ducks at their peak stage of egg production, 42,782,676 reads were obtained, with 4,307,499,083 bp sequenced. From ducks at their late stage of egg production, 45,316,166 reads were obtained, with 4,562,063,363 bp sequenced. A comparison of the two datasets identified 2,002 differentially expressed genes, with 790 upregulated and 1,212 downregulated. Further analysis showed that 1,645 of the 2,002 differentially expressed genes were annotated in the non-redundant (NR) database, with 646 upregulated and 999 downregulated. Among the differentially expressed genes with annotations in the NR database, 696 genes were functionally annotated in the clusters of orthologous groups of proteins database, involving 25 functional categories. One thousand two hundred four of the differentially expressed genes with annotations in the NR database were functionally annotated in the gene ontology (GO) database, and could be divided into three domains and 56 categories. The three domains were cellular component, molecular function, and biological process. Among the genes identified in the GO database, 451 are involved in development and reproduction. Analysis of the differentially expressed genes with annotations in the NR database against the Kyoto encyclopedia of genes and genomes database revealed that 446 of the genes could be assigned to 175 metabolic pathways, of which the peroxisome proliferator-activated receptor signaling pathway, insulin signaling pathway, fructose and mannose metabolic pathways, gonadotropin releasing hormone signaling pathway and transforming growth factor beta signaling pathway were significantly enriched. Conclusion: The differences in ovarian transcriptomes in Shan Ma ducks between their peak and late stages of egg production were elucidated, which greatly enriched the ovarian transcriptomic information of egg-producing ducks.

• Journal of Life Science
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• v.12 no.5
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• pp.610-621
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• 2002

Conserved genes are importantly used to understand the major function in survival and replication of living organism. This study was focused on identification of conserved genes in microbial species and measuring the degree of conservation. For this purpose, in silico analysis was performed to search conserved genes based on the conservation level within microbial species. The ortholog list of COGs (Clusters of Orthologous Groups of proteins) in NCBI was used and whole genomes of 43 microbial species were included in that list. The distance value, derived from CLUSTALW multiple alignment program, was used as a descriptor of the conservation level of orthologs. It was revealed that 43 microbial genomes hold 72 conserved orthologs in common. The majority(72.2%) of the conserved genes was related to "translation, ribosomal structure and biogenesis" functional category. A GTPase-translation elogation factor(COG0050) was the best conserved gene from the distance value analysis. The 72 conserved genes, found in this research, would be useful not only to study minimal function genes but also new drug target among pathogens and to make a model of the virtual cell.tual cell.