• Mycobiology
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• v.49 no.3
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• pp.294-296
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• 2021

An endolichenic fungus, Xylaria grammica strain EL000614, showed strong nematicidal effects against plant pathogenic nematode, Meloidogyne incognita by producing grammicin. We report genome assembly of X. grammica EL000614 comprised of 25 scaffolds with a total length of 54.73 Mb, N50 of 4.60 Mb, and 99.8% of BUSCO completeness. GC contents of this genome were 44.02%. Gene families associated with biosynthesis of secondary metabolites or regulatory proteins were identified out of 13,730 gene models predicted.

• Journal of Animal Science and Technology
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• v.63 no.1
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• pp.194-197
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• 2021

Salmonella enterica is a representative foodborne pathogen in the world. The S. enterica strain K_SA184 was isolated from the lamb (Ovis aries), which was collected from a local traditional market in South Korea. In this study, the S. enterica strain K_SA184 was sequenced using PacBio RS II and Illumina NextSeq 500 platforms. The final complete genome of the S. enterica strain K_SA184 consist of one circular chromosome (4,725,087 bp) with 52.3% of guanine + cytosine (G + C) content, 4,363 of coding sequence (CDS), 85 of tRNA, and 22 of rRNA genes. The S. enterica strain K_SA184 genome includes encoding virulence genes, such as Type III secretion systems and multidrug resistance related genes.

• Journal of Animal Science and Technology
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• v.63 no.2
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• pp.461-464
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• 2021

Escherichia coli normally colonizes the lower intestine of animals and humans, but some serotypes are foodborne pathogens. The Escherichia coli K_EC180 was isolated from swine feces that were collected from a weaner pig. In this genome announcement, E. coli K_EC180 was sequenced using PacBio RS II and Illumina NextSeq 500 platforms. The complete chromosome of E. coli K_EC180 is composed of one circular chromosome (5,017,281 bp) with 50.4% of guanine + cytosine (G + C) content, 4,935 of coding sequence (CDS), 88 of tRNA, and 22 of rRNA genes. The complete genome of E. coli K_EC180 contains the toxin genes such as shiga-like toxins (stxA and stxB).

• Journal of Animal Science and Technology
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• v.66 no.1
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• pp.232-236
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• 2024

Ligilactobacillus is a genus of Gram-positive lactobacilli commonly found in the intestinal tracts of vertebrates. It has been granted a Qualified Presumption of Safety (QPS) status from the European Food Safety Authority (EFSA). One specific strain, Ligilactobacillus salivarius B4311, was isolated from fecal samples of broiler chickens from a farm associated with Chung-Ang University (Anseong, Korea). This strain was observed to have inhibitory effects against Listeria monocytogenes. In this paper, we present the complete genome sequence of Lig. salivarius B4311. The whole genome of strain B4311 comprises 2,071,255 bp assembled into 3 contigs representing a chromosome, repA-type megaplasmid, and small plasmid. The genome contains 1,963 protein-coding sequences, 22 rRNA genes, and 78 tRNA genes, with a guanine + cytosine (GC) content of 33.1%. The megaplasmid of strain B4311 was found to contain the bacteriocin gene cluster for salivaricin P, a two-peptide bacteriocin belonging to class IIb.

• Microbiology and Biotechnology Letters
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• v.46 no.3
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• pp.300-312
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• 2018

Whole-genome sequencing of the wood-rotting fungus, Flammulina fennae, was carried out to identify carbohydrate-active enzymes (CAZymes). De novo genome assembly (31 kmer) of short reads by next-generation sequencing revealed a total genome length of 32,423,623 base pairs (39% GC). A total of 11,591 gene models in the assembled genome sequence of F. fennae were predicted by ab initio gene prediction using the AUGUSTUS tool. In a genome-wide comparison, 6,715 orthologous groups shared at least one gene with F. fennae and 10,667 (92%) of 11,591 genes for F. fennae proteins had orthologs among the Dikarya. Additionally, F. fennae contained 23 species-specific genes, of which 16 were paralogous. CAZyme identification and annotation revealed 513 CAZymes, including 82 auxiliary activities, 220 glycoside hydrolases, 85 glycosyltransferases, 20 polysaccharide lyases, 57 carbohydrate esterases, and 45 carbohydrate binding-modules in the F. fennae genome. The genome information of F. fennae increases the understanding of this basidiomycete fungus. CAZyme gene information will be useful for detailed studies of lignocellulosic biomass degradation for biotechnological and industrial applications.

• Journal of Animal Science and Technology
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• v.64 no.1
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• pp.183-186
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• 2022

Lactiplantibacillus plantarum (L. plantarum) ST was isolated from De'ang pickled tea in Yunnan Province, China. The genomes of strain ST were fully sequenced and analyzed using the PacBio RS II sequencing system. Our previous study has shown that L. plantarum ST is a potential probiotic strain. It had strong tolerance in the simulated artificial gastrointestinal tract, and in the antagonism tests, this strain showed strong antibacterial activity. Therefore, as a probiotic, it may be used in animal breeding. L. plantarum ST genome was composed of 1 circular chromosome and 7 plasmids. The length of the whole genome was 3320817 bp, and the annular chromosome size was 3058984 bp, guanine + cytosine (G ± C) content (%) was 44.76%, which contained 2945 protein-coding sequences (CDS). This study will contribute to a further comprehensive understanding of L. Plantarum ST at the genomic level and provide a theoretical basis for its future application in animal breeding.

• Molecules and Cells
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• v.37 no.1
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• pp.36-42
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• 2014

The tomato (Solanum lycopersicum L.) is a model plant for genome research in Solanaceae, as well as for studying crop breeding. Genome-wide single nucleotide polymorphisms (SNPs) are a valuable resource in genetic research and breeding. However, to do discovery of genome-wide SNPs, most methods require expensive high-depth sequencing. Here, we describe a method for SNP calling using a modified version of SAMtools that improved its sensitivity. We analyzed 90 Gb of raw sequence data from next-generation sequencing of two resequencing and seven transcriptome data sets from several tomato accessions. Our study identified 4,812,432 non-redundant SNPs. Moreover, the workflow of SNP calling was improved by aligning the reference genome with its own raw data. Using this approach, 131,785 SNPs were discovered from transcriptome data of seven accessions. In addition, 4,680,647 SNPs were identified from the genome of S. pimpinellifolium, which are 60 times more than 71,637 of the PI212816 transcriptome. SNP distribution was compared between the whole genome and transcriptome of S. pimpinellifolium. Moreover, we surveyed the location of SNPs within genic and intergenic regions. Our results indicated that the sufficient genome-wide SNP markers and very sensitive SNP calling method allow for application of marker assisted breeding and genome-wide association studies.

• Proceedings of the Korean Biophysical Society Conference
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• 2003.06a
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• pp.20-20
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• 2003

The success of genome project brought us a vast amount of sequence information about whole genes for some species. In order to get functional understanding of un-annotated genes, a number of frontiers in structural biology proposed a new paradigm for structural research on the basis of given information. Structural biologists believe that the whole characters of the living cells come from the protein functions, which could be regulated by three-dimensional protein structures.

• Genomics & Informatics
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• v.21 no.3
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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.

• Plant Breeding and Biotechnology
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• v.5 no.4
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• pp.269-281
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• 2017

With the continual development of genetically modified (GM) crops, it has become necessary to develop detailed and effective molecular characterization methods to select candidate events from a large pool of transformation events. Relative to traditional molecular analysis methods such as the polymerase chain reaction (PCR) and Southern blot hybridization, next generation sequencing (NGS) technology for whole-genome sequencing of complex crop genomes had proven comparatively useful for in-depth molecular characterization. In this study, four transformation events, including one in Bacillus thuringiensis (Bt)-resistant rice, one in resveratrol-producing rice, and two in beta-carotene-enhanced soybeans, were selected for molecular characterization. To merge NGS analysis and Southern blot-hybridization results, we confirmed the transgene insertion sites, insertion construction, and insertion numbers of these four transformation events. In addition, the read-coverage depth assessed by NGS analysis for inserted genes might provide consistent results in terms of inserted T-DNA numbers in case of complex insertion structures and highly duplicated donor genomes; however, PCR-based methods can produce incorrect conclusions. Our combined method provides an effective and complete analytical approach for whole-genome visual inspection of transformation events that require biosafety assessment.