• Journal of Microbiology and Biotechnology
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• v.27 no.4
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• pp.825-833
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• 2017

Strain IMCC26207 was isolated from the surface layer of Lake Soyang in Korea by the dilutionto-extinction culturing method, using a liquid medium prepared with filtered and autoclaved lake water. The strain could neither be maintained in a synthetic medium other than natural freshwater medium nor grown on solid agar plates. Phylogenetic analysis of 16S rRNA gene sequences indicated that strain IMCC26207 formed a distinct lineage in the order Acidimicrobiales of the phylum Actinobacteria. The closest relative among the previously identified bacterial taxa was "Candidatus Microthrix parvicella" with 16S rRNA gene sequence similarity of 91.7%. Here, the draft genome sequence of strain IMCC26207, a freshwater actinobacterium, is reported with the description of the genome properties and annotation summary. The draft genome consisted of 10 contigs with a total size of 3,316,799 bp and an average G+C content of 57.3%. The IMCC26207 genome was predicted to contain 2,975 protein-coding genes and 51 non-coding RNA genes, including 45 tRNA genes. Approximately 76.8% of the protein coding genes could be assigned with a specific function. Annotation of the IMCC26207 genome showed several traits of adaptation to living in oligotrophic freshwater environments, such as phosphorus-limited condition. Comparative genomic analysis revealed that the genome of strain IMCC26207 was distinct from that of "Candidatus Microthrix" strains; therefore, we propose the name "Candidatus Limnosphaera aquatica" for this bacterium.

• Journal of Plant Biotechnology
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• v.37 no.2
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• pp.153-165
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• 2010

Brassica rapa is considered an ideal candidate to act as a reference species for Brassica genomic studies. Among the three basic Brassica species, B. rapa (AA genome) has the smallest genome (529 Mbp), compared to B. nigra (BB genome, 632 Mbp) and B. oleracea (CC genome, 696 Mbp). There is also a large collection of available cultivars of B. rapa, as well as a broad array of B. rapa genomic resources available. Under international consensus, various genomic studies on B. rapa have been conducted, including the construction of a physical map based on 22.5X genome coverage, end sequencing of 146,000 BACs, sequencing of >150,000 expressed sequence tags, and successful phase 2 shotgun sequencing of 589 euchromatic region-tiling BACs based on comparative positioning with the Arabidopsis genome. These sequenced BACs mapped onto the B. rapa genome provide beginning points for genome sequencing of each chromosome. Applying this strategy, all of the 10 chromosomes of B. rapa have been assigned to the sequencing centers in seven countries, Korea, UK, China, India, Canada, Australia, and Japan. The two longest chromosomes, A3 and A9, have been sequenced except for several gaps, by NAAS in Korea. Meanwhile a China group, including IVF and BGI, performed whole genome sequencing with Illumina system. These Sanger and NGS sequence data will be integrated to assemble a draft sequence of B. rapa. The imminent B. rapa genome sequence offers novel insights into the organization and evolution of the Brassica genome. In parallel, the transfer of knowledge from B. rapa to other Brassica crops would be expected.

• Microbiology and Biotechnology Letters
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• v.51 no.4
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• pp.551-554
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• 2023

We report the draft genome sequence of Sporobolomyces phaffii RJAF-17, a basidiomycetous yeast strain producing lipoamino acid surfactants, N-palmitoyl leucine and N-parmitoleyl glutamine. The annotation and classification of protein-coding genes provided the basic information for the genome of strain RJAF-17, including prediction of abundant genes as well as detection of genes involved in the biosynthesis of lipoamino acids. With the molecular importance of lipoamino acids as promising alternatives to chemical surfactants, the genomic information of strain RJAF-17 can help us understand the role of biomolecules in yeasts and explore possibilities of large-scale synthesis for industrial applications.

• Korean Journal of Microbiology
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• v.55 no.1
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• pp.80-82
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• 2019

Pseudomonas syringae pv. syringae strain WSPS007 was isolated from infected twigs (Malus pumila) in 2013 in Yeongju, Gyeongbuk Province, Republic of Korea. Here, we report the draft genome sequence of WSPS007 with a chromosome size of 6,238,498 bp (59.04% G+C content). The genome comprises 5,379 CDS, 16 rRNA genes, and 65 tRNA genes. The P. syringae pv. syringae strain WSPS007 genome possesses an ice-nucleating activation (INA) gene and an antifreeze operon that may be related to frost damage by this pathogen. Thus, the genome sequence determined in this study will be useful in understanding the relationship between the outbreak of bacterial shoot blight disease and frost damage in northern Gyeongbuk Province.

• Korean Journal of Microbiology
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• v.54 no.2
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• pp.158-160
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• 2018

Streptomyces sp. P3 was isolated from potato scab diseased tubers in Pyeongchang, Gangwon-do, Republic of Korea in 2017. Here, we report the draft genome sequences of P3 with 9,851,971 bp size (71.2% GC content) of the chromosome. The genome comprises 8,548 CDS, 18 rRNA and 66 tRNA genes. Although strain P3 did not show pathogenicity both potato tuber assay and radish seedling assay, it possesses tomatinase (tomA) gene among conserved pathogenicity-related genes in well characterized pathogenic Streptomyces. Thus, the genome sequences determined in this study will be useful to understand for pathogenic evolution in Streptomyces species, which already adapted to potato scab pathogens.

• Korean Journal of Microbiology
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• v.54 no.1
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• pp.71-73
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• 2018

Recently, Fusobacterium nucleatum subsp. polymorphum was reclassified as Fusobacterium polymorphum based on the average nucleotide identity and genome-to-genome distance analyses. F. polymorphum is a Gram-negative, anaerobic, and filament-shaped bacterium. F. polymorphum is a part of normal flora of oral cavity and causative agent of periodontal diseases. F. polymorphum KCOM 1001 (= ChDC F119) was isolated from a human subgingival plaque of gingivitis lesion. Here, we present the complete genome sequence of F. polymorphum KCOM 1001.

• Korean Journal of Microbiology
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• v.53 no.3
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• pp.222-224
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• 2017

Prevotella intermedia is a Gram-negative, obligately anaerobic, nonsporeforming, and nonmotile rod. P. intermedia is associated with periodontitis, pregnancy gingivitis, acute necrotic ulcerative gingivitis, endodontic infection, and rheumatoid arthritis. P. intermedia KCOM 1107 (= ChDC KB29) was isolated from a human subgingival dental plaque of gingivitis lesion. Here, we present the draft genome sequence of P. intermedia KCOM 1107.

• Korean Journal of Microbiology
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• v.54 no.2
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• pp.146-148
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• 2018

Fusobacterium animalis (formerly Fusobacterium nucleatum subsp. animalis) is a Gram-negative, anaerobic, and filament-shaped bacterium. F. animalis may be a part of normal flora and a periodontopathogen of human oral cavity. F. animalis KCOM 1280 (= ChDC F318) was isolated from a human periodontitis lesion. In this report, we present the draft genome sequence of F. animalis KCOM 1280.

• Korean Journal of Microbiology
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• v.53 no.4
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• pp.334-336
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• 2017

Porphyromonas gingivalis is a Gram-negative, obligately anaerobic, and nonmotile rod. P. gingivalis is a pathogen of periodontitis and endodontic infection as well as is associated with systemic diseases including atherosclerosis, preterm, and Alzheimer's diseases. P. gingivalis KCOM 2797 (= JS2) was isolated from a human periodontitis lesion. Here, we present the draft genome sequence of P. gingivalis KCOM 2797.

• Korean Journal of Microbiology
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• v.55 no.1
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• pp.67-68
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• 2019

Streptococcus constellatus is Gram-stain-positive, facultative anaerobic, and non-spore forming coccus. It is a member of normal flora of human oral cavity. S. constellatus KCOM 1039 was isolated from human postoperative maxillary cyst lesion. In this report, we present the draft genome sequence of S. constellatus KCOM 1039.