• Mycobiology
• /
• v.50 no.1
• /
• pp.66-78
• /
• 2022

The identification of oleaginous yeast species capable of simultaneously utilizing xylose and glucose as substrates to generate value-added biological products is an area of key economic interest. We have previously demonstrated that the Cutaneotrichosporon dermatis NICC30027 yeast strain is capable of simultaneously assimilating both xylose and glucose, resulting in considerable lipid accumulation. However, as no high-quality genome sequencing data or associated annotations for this strain are available at present, it remains challenging to study the metabolic mechanisms underlying this phenotype. Herein, we report a 39,305,439 bp draft genome assembly for C. dermatis NICC30027 comprised of 37 scaffolds, with 60.15% GC content. Within this genome, we identified 524 tRNAs, 142 sRNAs, 53 miRNAs, 28 snRNAs, and eight rRNA clusters. Moreover, repeat sequences totaling 1,032,129 bp in length were identified (2.63% of the genome), as were 14,238 unigenes that were 1,789.35 bp in length on average (64.82% of the genome). The NCBI non-redundant protein sequences (NR) database was employed to successfully annotate 11,795 of these unigenes, while 3,621 and 11,902 were annotated with the Swiss-Prot and TrEMBL databases, respectively. Unigenes were additionally subjected to pathway enrichment analyses using the Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Cluster of Orthologous Groups of proteins (COG), Clusters of orthologous groups for eukaryotic complete genomes (KOG), and Non-supervised Orthologous Groups (eggNOG) databases. Together, these results provide a foundation for future studies aimed at clarifying the mechanistic basis for the ability of C. dermatis NICC30027 to simultaneously utilize glucose and xylose to synthesize lipids.

• Korean Journal of Microbiology
• /
• v.55 no.1
• /
• pp.74-76
• /
• 2019

Gram-positive anaerobic bacilli Actinomyces spp. commonly reside on mucosal surfaces of the oropharynx, gastrointestinal tract, and urogenital tract. Here, we first report the draft genome sequence of Actinomyces georgiae KHUD_A1, isolated from dental plaque of a Korean elderly woman. The genome is 2,652,059 bp in length and has a GC content of 68.06%. The genome includes 2,242 protein-coding genes, 9 rRNAs, and 64 tRNA. We identified 157 KHUD_A1 strain-specific genes, including genes encoding CPBP family intramembrane metalloprotease, bile acid: sodium symporter family protein, Txe/YoeB family addiction module toxin and Phd/YefM family antitoxin. The sequence information of A. georgiae KHUD_A1 will help understand the general characteristics of the bacterial species and the genome diversity of the genus Actinomyces.

• Proceedings of the Korean Society of Crop Science Conference
• /
• 2017.06a
• /
• pp.141-141
• /
• 2017

The ubiquitin-proteasome pathway is the major regulatory mechanism in a number of cellular processes for selective degradation of proteins and involves three steps: (1) ATP dependent activation of ubiquitin by E1 enzyme, (2) transfer of activated ubiquitin to E2 and (3) transfer of ubiquitin to the protein to be degraded by E3 complex. F-box proteins are subunit of SCF complex and involved in specificity for a target substrate to be degraded. F-box proteins regulate many important biological processes such as embryogenesis, floral development, plant growth and development, biotic and abiotic stress, hormonal responses and senescence. However, little is known about the F-box genes in wheat. The draft genome sequence of wheat (IWGSC Reference Sequence v1.0 assembly) used to analysis a genome-wide survey of the F-box gene family in wheat. The Hidden Markov Model (HMM) profiles of F-box (PF00646), F-box-like (PF12937), F-box-like 2 (PF13013), FBA (PF04300), FBA_1 (PF07734), FBA_2 (PF07735), FBA_3 (PF08268) and FBD (PF08387) domains were downloaded from Pfam database were searched against IWGSC Reference Sequence v1.0 assembly. RNA-seq paired-end libraries from different stages of wheat, such as stages of seedling, tillering, booting, day after flowering (DAF) 1, DAF 10, DAF 20, and DAF 30 were conducted and sequenced by Illumina HiSeq2000 for expression analysis of F-box protein genes. Basic analysis including Hisat, HTseq, DEseq, gene ontology analysis and KEGG mapping were conducted for differentially expressed gene analysis and their annotation mappings of DEGs from various stages. About 950 F-box domain proteins identified by Pfam were mapped to wheat reference genome sequence by blastX (e-value < 0.05). Among them, more than 140 putative F-box protein genes were selected by fold changes cut-offs of > 2, significance p-value < 0.01, and FDR<0.01. Expression profiling of selected F-box protein genes were shown by heatmap analysis, and average linkage and squared Euclidean distance of putative 144 F-box protein genes by expression patterns were calculated for clustering analysis. This work may provide valuable and basic information for further investigation of protein degradation mechanism by ubiquitin proteasome system using F-box proteins during wheat development stages.

• Journal of Marine Life Science
• /
• v.6 no.1
• /
• pp.38-46
• /
• 2021

The blood clam, Tegillarca granosa, is economically important in marine bivalve and is used in fisheries industry among western Pacific Ocean Coasts especially in Korea, China, and Japan. The number of chromosomes in the blood clam is known as 2n=38, but the genome size and genetic information of the genome are not still clear. In order to predict the genomic size of the T. granosa, the in-silico analysis analysed the genomic size using short DNA sequence information obtained using the NGS Illumina HiSeq platform. As a result, the genomic size of T. granosa was estimated to be 770.61 Mb. Subsequently, a draft genome assembly was performed through the MaSuRCA assembler, and a simple sequence repeat (SSR) analysis was done by using the QDD pipeline. 43,944 SSRs were detected from the genome of T. granosa and 69.51% di-nucleotide, 16.68% trinucleotide, 12.96% tetra-nucleotide, 0.82% penta-nucleotide, and 0.03% hexa-nucleotide were consisted. 100 primer sets that could be used for genetic diversity studies were selected. In the future, this study will help identify the genetic diversity of T. granosa and population genetic studies, and further identify the classification of origin between homogenous groups.

• Proceedings of the Korean Society for Bioinformatics Conference
• /
• 2001.10a
• /
• pp.61-86
• /
• 2001

All cancers are caused by abnormalities in DNA sequence. Throughout life, the DNA in human cells is exposed to mutagens and suffers mistakes in replication, resulting in progressive, subtle changes in the DNA sequence in each cell. Since the development of conventional and molecular cytogenetic methods to the analysis of chromosomal aberrations in cancers, more than 1,800 recurring chromosomal breakpoints have been identified. These breakpoints and regions of nonrandom copy number changes typically point to the location of genes involved in cancer initiation and progression. With the introduction of molecular cytogenetic methodologies based on fluorescence in situ hybridization (FISH), namely, comparative genomic hybridization (CGH) and multicolor FISH (m-FISH) in carcinomas become susceptible to analysis. Conventional CGH has been widely applied for the detection of genomic imbalances in tumor cells, and used normal metaphase chromosomes as targets for the mapping of copy number changes. However, this limits the mapping of such imbalances to the resolution limit of metaphase chromosomes (usually 10 to 20 Mb). Efforts to increase this resolution have led to the "new"concept of genomic DNA chip (1 to 2 Mb), whereby the chromosomal target is replaced with cloned DNA immobilized on such as glass slides. The resulting resolution then depends on the size of the immobilized DNA fragments. We have completed the first draft of its Korean Genome Project. The project proceeded by end sequencing inserts from a library of 96,768 bacterial artificial chromosomes (BACs) containing genomic DNA fragments from Korean ethnicity. The sequenced BAC ends were then compared to the Human Genome Project′s publicly available sequence database and aligned according to known cancer gene sequences. These BAC clones were biotinylated by nick translation, hybridized to cytogenetic preparations of metaphase cells, and detected with fluorescein-conjugated avidin. Only locations of unique or low-copy Portions of the clone are identified, because high-copy interspersed repetitive sequences in the probe were suppressed by the addition of unlabelled Cotl DNA. Banding patterns were produced using DAPI. By this means, every BAC fragment has been matched to its appropriate chromosomal location. We have placed 86 (156 BAC clones) cytogenetically defined landmarks to help with the characterization of known cancer genes. Microarray techniques would be applied in CGH by replacement of metaphase chromosome to arrayed BAC confirming in oncogene and tumor suppressor gene: and an array BAC clones from the collection is used to perform a genome-wide scan for segmental aneuploidy by array-CGH. Therefore, the genomic DNA chip (arrayed BAC) will be undoubtedly provide accurate diagnosis of deletions, duplication, insertions and rearrangements of genomic material related to various human phenotypes, including neoplasias. And our tumor markers based on genetic abnormalities of cancer would be identified and contribute to the screening of the stage of cancers and/or hereditary diseases

• Journal of Microbiology and Biotechnology
• /
• v.28 no.10
• /
• pp.1760-1768
• /
• 2018

The type strain Bacillus subtilis subsp. subtilis KCTC $3135^T$ was deeply sequenced and annotated, replacing a previous draft genome in this study. The tar and tag genes were involved in synthesizing wall teichoic acids (WTAs), and these genes and their products were previously regarded as the distinguishing difference between B. s. subtilis and B. s. spizizenii. However, a comparative genomic analysis of B. subtilis spp. revealed that both B. s. subtilis and B. s. spizizenii had various types of cell walls. These tar and tag operons were mutually exclusive and the tar genes from B. s. spizizenii were very similar to the genes from non-Bacillus bacteria, unlike the tag genes from B. s. subtilis. The results and previous studies suggest that the tar genes and the tag genes are not inherited after subspecies speciation. The phylogenetic tree based on whole genome sequences showed that each subspecies clearly formed a monophyletic group, while the tree based on tar genes showed that monophyletic groups were formed according to the cell wall type rather than the subspecies. These findings indicate that the tar genes and the presence of ribitol as a cell-wall constituent were not the distinguishing difference between the subspecies of B. subtilis and that the description of subspecies B. s. spizizenii should be updated.

• Korean Journal of Microbiology
• /
• v.53 no.2
• /
• pp.141-143
• /
• 2017

Caballeronia sordidicola strain PAMC 26577 was isolated from Cladonia sp., a lichen collected from Svalbard Archipelago in the Arctic Ocean. Draft genomic sequences of PAMC 26577 were determined using Illumina and 182 contigs were submitted to GenBank and N50 value was 159,226. The genome of PAMC 26577 was comprised of 8,334,211 base pairs and %G+C content was 59.4. The genome included 8 ribosomal RNA genes and 51 tRNA genes as non-coding sequences. Protein-coding genes were 8,065 in number and they included central metabolism genes as well as butanol/butyrate biosynthesis, polyhydroxybutyrate metabolism, serine cycle methylotrophy genes, and glycogen metabolism. Membrane transporters were more than two-hundreds in number, but sugar phosphotransferase system and TRAP transporters were lacking. PAMC 26577 lacked CRISPR-associated sequences and proteins. No transposable elements were observed and there were only limited number of phage remnant regions with 11 phage-related genes.

• Korean Journal of Microbiology
• /
• v.54 no.3
• /
• pp.302-304
• /
• 2018

We, for the first time, isolated and identified a Vibrio splendidus KCTC 11899BP producing hyaluronate lyase from seawater. This enzyme is produced only when hyaluronic acid (HA) is added to the basal medium. Hyaluronate lyases are produced by microorganisms, which degrade the ${\beta}$-(1, 4) bond of HA to produce disaccharide. The genome of KCTC 11899BP, which consist of two circular contigs that are 3,522 kb (contig 1) long and 1,986 kb (contig 2) long respectively, as like other Vibrio sp. that contained 2 chromosomes. The genome included 4,700 predicted open reading frames, G + C content 44.12%, 137 tRNA genes, and 46 rRNA genes.

• The Korean Journal of Pesticide Science
• /
• v.17 no.4
• /
• pp.468-472
• /
• 2013

Chrysanthemum is an economically important horticultural plant in many countries. The white rust is one of the most devastating diseases caused by an obligate fungal pathogen Puccinia horiana. This is being controlled mostly by application of chemicals. In Korea, 26 items are registered and 10 items contain 6 triazole compounds. To identify and to obtain the information of the drug target for triazoles, possible sterol 14-demethylase orthologues were extracted. From the draft genome information, the nucleotide sequence of the sterol 14-demethylase gene was identified. The amino acid sequence was deduced and the tertiary structure of the enzyme was predicted. This protein showed no less than 84% amino acid sequence identities to those of genus Puccinia and no more than 68% to those of other genus.

• Korean Journal of Microbiology
• /
• v.55 no.2
• /
• pp.160-163
• /
• 2019

Senegalimassilia sp. KGMB 04484 was isolated from fecal samples obtained from a healthy Korean. The whole-genome sequence of Senegalimassilia sp. KGMB 04484 was analyzed using the PacBio Sequel platform. The genome comprises a 2,748,041 bp chromosome with a G+C content of 61.18%, 2,300 total genes, 2,139 protein-coding gene, 21 rRNA genes, and 51 tRNA genes. Also, we found that strain KGMB 04484 had some genes for hydrolysis enzyme, fatty acid biosynthesis and metabolism in its genome based on the result of genome analysis. Those genes of KGMB 04484 may be related to regulation of human health and digest.