• Mycobiology
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• v.48 no.6
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• pp.528-531
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• 2020

Scopulariopsis brevicaulis is a widely distributed soil fungus known as a common saprotroph of biodegradation. It is also an opportunistic human pathogen that can produce various secondary metabolites. Here, we report the first complete mitochondrial genome sequence of S. brevicaulis isolated from air in South Korea. Total length of the mitochondrial genome is 28,829 bp and encoded 42 genes (15 protein-coding genes, 2 rRNAs, and 25 tRNAs). Nucleotide sequence of coding region takes over 26.2%, and overall GC content is 27.6%. Phylogenetic trees present that S. brevicaulis is clustered with Lomentospora prolificans with presenting various mitochondrial genome length.

• Korean Journal of Microbiology
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• v.55 no.1
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• pp.77-79
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• 2019

Here we report the genome sequence of Veillonella atypica strain KHUD-V1 isolated from subgingival dental plaque of Korean chronic periodontitis patients. Unlike other V. atypica strains, KHUD-V1 carries two prophage regions and prophage remnants, as well as several genes homologous to prophage-associated virulence factors, such as virulence-associated protein E, a Clp protease, and a toxin-antitoxin system. The isolate and its genome sequence obtained here will aid to understand the diversity of the genome architecture of Veillonella within an evolutionary framework and the role of prophages that contribute to the genetic diversity as well as the virulence of V. atypica.

• Korean Journal of Agricultural Science
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• v.31 no.1
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• pp.35-44
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• 2004

In this study, the automatic system exchanging well-plates was developed as a basic stage of the genome project. The developed system consisted of the plate fixing well-plates, the well-plate cassette, the head to move a well-plate from the well-plate cassette to the plate fixing well-plates before genome work or from the plate to the cassette after the work, the manipulator to move the head on the X, Y and Z axes and the control system. The performance test to exchange well-plates with the robotic system developed was carried out. The time to set an well-plate from the well-plate cassette onto the board fixing well-plates was 55 seconds and the time for 9 ones was 8 minutes and 15 seconds. It took 57 seconds to move a well-plate from the board to the cassette and 8 minutes and 33 seconds for 9 ones.

• Korean Journal of Microbiology
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• v.55 no.3
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• pp.300-302
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• 2019

Glutamicibacter halophytocola DR408 isolated from the rhizospheric soil of soybean plant at Jecheon showed drought tolerance and plant growth promotion capacity. The complete genome of strain DR408 comprises 3,770,186 bp, 60.2% GC-content, which include 3,352 protein-coding genes, 64 tRNAs, 19 rRNA, and 3 ncRNA. The genome analysis revealed gene clusters encoding osmolyte synthesis and plant growth promotion enzymes, which are known to contribute to improve drought tolerance of the plant.

• Journal of Microbiology and Biotechnology
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• v.16 no.1
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• pp.32-36
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• 2006

The genome sequences from several microbes have led to the discovery of numerous open reading frames of unknown functionality. The putative bacterial epoxide hydrolase (EH) genes selected from the genome databases were examined for their activities toward various epoxides. Among the nine open reading frames (ORFs) from four microbial species, the ORF from Caulobacter crescentus showed an epoxide hydrolase activity. The kinetic resolution, using C. crescentus EH (CCEH) of the aryl epoxides such as styrene oxide, could be performed more efficiently than short aliphatic epoxides. The resolution of racemic indene oxide, which could previously be resolved only by fungal epoxide hydrolases, was effectively accomplished by CCEH.

• Molecules and Cells
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• v.38 no.9
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• pp.743-749
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• 2015

Production of genome-edited animals using germline-competent cells and genetic modification tools has provided opportunities for investigation of biological mechanisms in various organisms. The recently reported programmed genome editing technology that can induce gene modification at a target locus in an efficient and precise manner facilitates establishment of animal models. In this regard, the demand for genome-edited avian species, which are some of the most suitable model animals due to their unique embryonic development, has also increased. Furthermore, germline chimera production through longterm culture of chicken primordial germ cells (PGCs) has facilitated research on production of genome-edited chickens. Thus, use of avian germline modification is promising for development of novel avian models for research of disease control and various biological mechanisms. Here, we discuss recent progress in genome modification technology in avian species and its applications and future strategies.

• Journal of Genetic Medicine
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• v.20 no.1
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• pp.1-5
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• 2023

Until now, rare disease studies have mainly been carried out by detecting simple variants such as single nucleotide substitutions and short insertions and deletions in protein-coding regions of disease-associated gene panels using diagnostic next-generation sequencing in association with patient phenotypes. However, several recent studies reported that the detection rate hardly exceeds 50% even when whole-exome sequencing is applied. Therefore, the necessity of introducing whole-genome sequencing is emerging to discover more diverse genomic variants and examine their association with rare diseases. When no diagnosis is provided by whole-genome sequencing, additional omics techniques such as RNA-seq also can be considered to further interrogate causal variants. This paper will introduce a description of these multi-omics techniques and their applications in rare disease studies.

• Journal of Plant Biotechnology
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• v.43 no.4
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• pp.411-416
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• 2016

Next-generation sequencing allows the identification of mutations responsible for mutant phenotypes by whole-genome resequencing and alignment to a reference genome. However, when the resequenced cultivar/line displays significant structural variation from the reference genome, mutations in the genome regions absent in the reference cannot be identified by simple alignment. In this review, we report the current status and prospects in identification of genes in mutant phenotypes, by using the methods MutMap, MutMap-Gap, and MutMap+. These methods delineate a candidate region harboring a mutation of interest, followed by de novo assembly, alignment, and identification of the mutation within genome gaps. These methods are likely to prove useful for cloning genes that exhibit significant structural variations, such as disease resistance genes of the nucleotide-binding site-leucine rich repeat (NBS-LRR) class.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.49 no.6
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• pp.867-874
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• 2016

Although shrimps belonging to family Crangonidae are known to be genetically divergent and ecologically important among the various benthos, any of their mitochondrial genome has not been reported yet. We here determined the complete mitochondrial genome sequence of Crangon hakodatei (Rathbun, 1902), which was collected from East China Sea ($124^{\circ}E$ and $34.5^{\circ}N$). Total mitochondrial genome length of C. hakodatei was 16,060 bp, in which 13 proteins, 2 ribosomal RNAs, 22 transfer RNAs and a putative control region were encoded. Secondary structure prediction analysis showed that twenty tRNA genes exhibit the conserved structure but two genes, $tRNA^{Cys}$ and $tRNA^{Ser}$ (AGN), lack T and D arm, respectively. Based on the sequence similarity of the COI region from the currently reported five species belonging to genus Crangonidae, C. hakodatei was most closely related to Crangon crangon. Phylogenetic analysis of full COXI genes belonging to infraorder Caridea showed that only crangonid shrimps were clustered together with those of Dendrobranchiata. Gene order were well conserved from Penaeoidea to Caridea but $tRNA^{Pro}$ and $tRNA^{Thr}$ in Palaemonid shrimp were flipped each other by the recombination. Further study about mitochondrial genome sequences of shrimps belonging to Crangonidae should be made to know better about their evolutional relationships with other those in infraorder Caridea.

• Journal of Microbiology and Biotechnology
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• v.22 no.2
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• pp.184-189
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• 2012

We sought to breed an industrially useful yeast strain, specifically an ethanol-tolerant yeast strain that would be optimal for ethanol production, using a novel breeding method, called genome reconstruction, based on chromosome splitting technology. To induce genome reconstruction, Saccharomyces cerevisiae strain SH6310, which contains 31 chromosomes including 12 artificial mini-chromosomes, was continuously cultivated in YPD medium containing 6% to 10% ethanol for 33 days. The 12 mini-chromosomes can be randomly or specifically lost because they do not contain any genes that are essential under high-level ethanol conditions. The strains selected by inducing genome reconstruction grew about ten times more than SH6310 in 8% ethanol. To determine the effect of mini-chromosome loss on the ethanol tolerance phenotype, PCR and Southern hybridization were performed to detect the remaining mini-chromosomes. These analyses revealed the loss of mini-chromosomes no. 11 and no. 12. Mini-chromosome no. 11 contains ten genes (YKL225W, PAU16, YKL223W, YKL222C, MCH2, FRE2, COS9, SRY1, JEN1, URA1) and no. 12 contains fifteen genes (YHL050C, YKL050W-A, YHL049C, YHL048C-A, COS8, YHLComega1, ARN2, YHL046W-A, PAU13, YHL045W, YHL044W, ECM34, YHL042W, YHL041W, ARN1). We assumed that the loss of these genes resulted in the ethanol-tolerant phenotype and expect that this genome reconstruction method will be a feasible new alternative for strain improvement.