• Mycobiology
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• 제48권6호
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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.

• 미생물학회지
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• 제55권1호
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• pp.77-79
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• 2019

본 논문에서는 한국인 만성 치주염 환자의 치은연하치태에서 분리된 Veillonella atypica KHUD-V1의 유전체 서열을 보고한다. 다른 V. atypica 균주와 달리, KHUD-V1에서는 프로 파지 및 이와 관련된 것으로 추정되는 여러 병독성 인자가 확인되었다. V. atypica KHUD-V1 균주 및 이 균주의 유전체 서열정보는 Veillonella의 유전체 다양성을 진화론적 관점에서 이해하고, V. atypica의 병독성 및 유전적 다양성에 기여하는 프로파지의 역할을 연구하는데 유용할 것이다.

• 농업과학연구
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• 제31권1호
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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.

• 미생물학회지
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• 제55권3호
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• pp.300-302
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• 2019

제천에서의 콩 근권 시료로부터 분리한 Glutamicibacter halophytocola DR408 균주는 내건성 식물생장촉진력을 보이고 있다. 본 연구에서 DR408 균주의 완전한 유전체 서열을 해독한 결과, 유전체의 크기는 3.77 Mbp였으며, G + C 함량이 60.2%였다. 또한 총 3,352개의 유전자 서열과 65개의 tRNA, 19개의 rRNA, 3개의 ncRNA가 존재하였다. 유전체 분석을 통해 식물의 내건성을 향상시킬 수 있는 삼투질 합성과 식물생장촉진 효소를 코딩하는 유전자를 다수 포함하는 것을 확인하였다.

• Journal of Microbiology and Biotechnology
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• 제16권1호
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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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• 제38권9호
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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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• 제20권1호
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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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• 제43권4호
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• pp.411-416
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• 2016

NGS 기술은 전체 게놈 시퀀싱 및 reference 게놈에 alignment에 의해 돌연변이 표현형에 관련된 돌연변이 식별에 이용한다. 그러나 품종 및 계통들을 resequence 하였을 경우 기존의 reference 게놈에 구조적 변이가 보이며, reference와 맞지 않는 게놈지역에서 돌연변이들은 단순한 alignment로 찾을 수 없다. 본 리뷰에서는 NGS 기술을 이용하여 돌연변이체로부터 변이 관련 유전자를 식별하는 MutMap, MutMap-Gap 및 MutMap+ 방법을 기술하였고 지금까지의 연구현황에 대해 기술하였다. 아울러 이들 방법은 nucleotide-binding site-leucine rich repeat (NBS-LRR) 그룹들의 병 저항성 유전자와 같이 구조적 변이를 가진 유전자를 분리하는 등 유용성에 대해 고찰하였다.

• 한국수산과학회지
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• 제49권6호
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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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• 제22권2호
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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.