• 한국미생물·생명공학회지
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• 제51권3호
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• pp.300-302
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• 2023

This research presents the whole-genome sequence of Priestia megaterium S1, which was isolated from the soil of soybean (Glycine max). The genome of the strain is composed of a single chromosome with 5,297,673 bp, and the GC content is 38.12%.

• 한국잠사곤충학회지
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• 제42권2호
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• pp.126-141
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• 2000

A major step towards understanding of the genetic basis of an organism is the complete sequence determination of all genes in target genome. The nucleotide sequence encoded in the genome contains the information that specifies the amino acid sequence of every protein and functional RNA molecule. In principle, it will be possible to identify every protein resposible for the structure and function of the body of the target organism. The pattern of expression in different cell types will specify where and when each protein is used. The amino acid sequence of the proteins encoded by each gene will be derived from the conceptional translation of the nucleotide sequence. Comparison of these sequences with those of known proteins, whose sequences are sorted in database, will suggest an approximate function for many proteins. This mini review describes the development of new sequencing methods and the optimization of sequencing strategies for whole genome, various cDNA and genomic analysis.

• 한국미생물·생명공학회지
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• 제51권4호
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• pp.555-558
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• 2023

Staphylococcus aureus is a prominent multidrug-resistant pathogen known for its resistance to a variety of antibiotics. To combat this, a wide range of antibiotics, including quinolones, is utilized. While the efficacy of quinolones against S. aureus has been established, the rise in quinolone-resistant strains, particularly in methicillin-resistant S. aureus (MRSA), has necessitated a shift in their usage patterns. Genomic sequencing plays a crucial role as it offers insights into the genetic mechanisms of resistance. Thus, we report the complete genome sequence of an oxolinic acid-resistant strain of S. aureus isolated from sweet potato leaves, a crop commonly cultivated in Korea.

• 한국패류학회지
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• 제26권4호
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• pp.317-326
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• 2010

The availability of fast and inexpensive sequencing technology has enabled researchers around the world to conduct many genome sequencing and expressed sequence tag (EST) projects of diverse organisms. In recent years, whole genome projects have been undertaken to sequence ten species from the phylum Mollusca. These include Aplysia californica, Lottia gigantea, Crassostrea virginica, Spisula solidissima, Mytilus californianus, Biomphalaria glabrata, Crepidula fornicata, Elysia chlorotica, Lottia scutum and Radix balthica. Additionally, complete mitochondrial genomes of 91 mollusks have been reported. In Korea, EST projects have been conducted in nine mollusk species that include Nesiohelix samarangae, Pisidium (Neopisidium) coreanum, Physa acuta, Incilaria fruhstorferi, Meretrix lusoria, Ruditapes philippinarum, Nordotis gigantea, Crassostrea gigas and Laternula elliptica. Finally, the mitochondrial genome projects from the Pacific Oyster (Crassostrea gigas) and the rock shell (Thais clavigera) have been conducted and reported. However, no systemic mollusk genome project has so far been conducted in Korea. In this report, the current status and research trends in mollusk genome study in Korea will be discussed.

• 식물분류학회지
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• 제52권2호
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• pp.123-126
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• 2022

Hibiscus sabdariffa L., (roselle) in the Malvaceae family is an erect subshrub known to be native to India and Malaysia. It is widely used as a food or tea material around the world, and its therapeutic effects have been widely studied. In this study, the sequencing of the complete chloroplast genome of H. sabdariffa was carried out. The result indicates a genome size of 162,428 bp, which is composed of a large single copy of 90,327 bp, two inverted repeats of 26,242 bp each, and a small single copy of 19,617 bp. Overall, a total of 131 genes were predicted, including 86 coding sequences, 37 tRNAs, and 8 rRNAs. According to a phylogenic analysis, it was clearly distinguished from outgroups such as other species of the genus Hibiscus used in the analysis.

• 한국자원식물학회:학술대회논문집
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• 한국자원식물학회 2020년도 추계국제학술대회
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• pp.47-47
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• 2020

In this study, we aimed to study carnation italian ringspot virus (CIRV) in Erigeron annuus (L.) Pers. in Bonghwa County, Korea. The collected samples showed mosaic and malformation symptoms. To identify the virus species, we performed high-throughput sequencing, reverse transcription polymerase chain reaction, and cloning. The virus was confirmed to be an unreported species, and therefore we performed genome sequencing of the samples. The complete genome was 4,746 nucleotides in length. The CIRV contained five open reading frames (ORFs), and it showed the typical features of members of the genus Tombusvirus. Phylogenetic analyses revealed that ClRV isolates had the highest nucleotide identities with the CZ isolate (95.89%) from Korea. In recent years, these viruses have sporadically been reported in floral scent and medicinal plants. This research found the first natural host infected with CIRV, and provides baseline information to determine the correlation between weeds and crops.

• Journal of Microbiology and Biotechnology
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• 제29권5호
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• pp.794-808
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• 2019

Bacillus velezensis strain WRN014 was isolated from banana fields in Hainan, China. Bacillus velezensis is an important member of the plant growth-promoting rhizobacteria (PGPR) which can enhance plant growth and control soil-borne disease. The complete genome of Bacillus velezensis WRN014 was sequenced by combining Illumina Hiseq 2500 system and Pacific Biosciences SMRT high-throughput sequencing technologies. Then, the genome of Bacillus velezensis WRN014, together with 45 other completed genome sequences of the Bacillus velezensis strains, were comparatively studied. The genome of Bacillus velezensis WRN014 was 4,063,541bp in length and contained 4,062 coding sequences, 9 genomic islands and 13 gene clusters. The results of comparative genomic analysis provide evidence that (i) The 46 Bacillus velezensis strains formed 2 obviously closely related clades in phylogenetic trees. (ii) The pangenome in this study is open and is increasing with the addition of new sequenced genomes. (iii) Analysis of single nucleotide polymorphisms (SNPs) revealed local diversification of the 46 Bacillus velezensis genomes. Surprisingly, SNPs were not evenly distributed throughout the whole genome. (iv) Analysis of gene clusters revealed that rich gene clusters spread over Bacillus velezensis strains and some gene clusters are conserved in different strains. This study reveals that the strain WRN014 and other Bacillus velezensis strains have potential to be used as PGPR and biopesticide.

• 식물분류학회지
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• 제53권3호
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• pp.237-241
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• 2023

The genus Scrophularia L. (Scrophulariaceae) comprises 200-270 species worldwide and is a taxonomically challenging lineage, displaying morphological diversity and hybridization. S. kakudensis is morphologically similar to the closely related taxa S. kakudensis var. microphylla, S. pilosa, and S. cephalantha. Therefore, the purpose of this study was to sequence the chloroplast (cp) genome of S. kakudensis using next-generation sequencing and compare it to those of related taxa. The complete cp genome sequence of Scrophularia kakudensis was found to be 152,355 bp long, consisting of a pair of inverted repeats of 25,485 bp that separate a large single-copy (LSC) of 83,479 bp from small single-copy regions of 17,909 bp. The cp genome contained 78 protein-coding genes, 30 tRNAs, and four rRNAs. A phylogenetic analysis based on 78 protein-coding genes from six Scrophularia species showed S. kakudensis and S. cephalantha formed with 100% bootstrap values. We compared the complete cp genomes of S. kakudensis and S. cephalantha and identified seven sequence divergence regions: matK/rps16, rps16/trnQ, trnS/trnG, rpoB/trnC, trnS/trnG, rpl32/trnL, and ndhD/psaC. These regions may be useful for determining the phylogenetic relationships among S. kakudensis-related species.

• Journal of Animal Science and Technology
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• 제66권5호
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• pp.1079-1082
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• 2024

Treponema pedis, a fastidious anaerobic spirochete, is one of the main pathogens involved in the development and progression of bovine digital dermatitis (BDD), a lameness-causing hoof infection in cattle. Here, the complete genome sequencing of T. pedis GNW45 isolated from a dairy cow infected with BDD, was presented. Libraries for long and short reads were sequenced using PacBioRSII and Illimuna HiSeqXTen platforms, respectively. De-novo assembly was done using the long reads, producing a circular contig, by which the short reads were aligned to generate a more accurate genome sequence. The genome has a total size of 3,077,465 base pairs, with 36.84% guanine-cytosine content. A total of 2,749 protein-coding sequences, seven ribosomal RNA's, and 45 transfer RNA's were annotated. Functional analysis revealed genes associated with pathogenicity and survivability in the complex pathobiome of BDD. This study provided novel insights into the survival and pathogenic mechanisms of T. pedis GNW45.

• Genomics & Informatics
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• 제21권3호
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• pp.34.1-34.10
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• 2023

Nosocomial infections, commonly referred to as healthcare-associated infections, are illnesses that patients get while hospitalized and are typically either not yet manifest or may develop. One of the most prevalent nosocomial diseases in hospitalized patients is pneumonia, among the leading causes of mortality and morbidity. Viral, bacterial, and fungal pathogens cause pneumonia. More severe introductions commonly included Staphylococcus aureus, which is at the top of bacterial infections, per World Health Organization reports. The staphylococci, S. aureus, strain RMI-014804, mesophile, on-sporulating, and non-motile bacterium, was isolated from the sputum of a pulmonary patient in Pakistan. Many characteristics of S. aureus strain RMI-014804 have been revealed in this paper, with complete genome sequence and annotation. Our findings indicate that the genome is a single circular 2.82 Mbp long genome with 1,962 protein-coding genes, 15 rRNA, 49 tRNA, 62 pseudogenes, and a GC content of 28.76%. As a result of this genome sequencing analysis, researchers will fully understand the genetic and molecular basis of the virulence of the S. aureus bacteria, which could help prevent the spread of nosocomial infections like pneumonia. Genome analysis of this strain was necessary to identify the specific genes and molecular mechanisms that contribute to its pathogenicity, antibiotic resistance, and genetic diversity, allowing for a more in-depth investigation of its pathogenesis to develop new treatments and preventive measures against infections caused by this bacterium.