• 한국유기농업학회지
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• 제31권4호
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• pp.395-412
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• 2023

광식성 난방제 해충인 미국흰불나방(Hyphantria cunea)의 친환경 방제를 위한 바이러스 살충제의 소재 활용을 위해서 국내에서 분리된 미국흰불나방 핵다각체병바이러스(H. cunea nucleopolyhedrovirus W1: HycuNPV-W1)의 다각체 형태 및 전장 유전체 서열을 결정하고 분석하였다. HycuNPV-W1의 다각체는 1.5-2.2 um 크기의 사면체에 가까운 부정형으로 확인되었다. 전장 유전체의 염기서열을 결정한 결과, 기존에 보고된 HycuNPV와 비교할 때 1,606 bp 더 짧은 131,353 bp로 확인되었다. 그러나 G+C 함량은 45%였으며 상동반복영역은 6개로 기존에 보고된 HycuNPV와 차이는 확인할 수 없었다. ORF 분석에서는 HycuNPV-W1은 기존의 HycuNPV와 비교할 때 3개의 ORF가 더 적은 145개를 가졌으나, HycuNPV-W1에만 존재하는 2개의 ORF가 확인되었다. 이들 ORF의 기능은 현재까지 밝혀지지 않았으나 바이러스의 생물학적 특성에 큰 영향을 주지 않을 것으로 추정되었다. 유전체의 vista 분석 결과에서는 HycuNPV-W1과 기존 HycuNPV의 전체 염기서열 유사도가 매우 높은 것으로 확인되었다. 국내에서 처음으로 분석한 HycuNPV-W1의 전장 유전체는 기존의 HycuNPV와 매우 유사한 것으로 나타났으나, 독자적인 특성을 가진 서로 다른 분리주로 국내 고유자원임을 확인할 수 있었다.

• Molecules and Cells
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• 제38권6호
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• pp.475-481
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• 2015

Programmable nucleases, which include zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and RNA-guided engineered nucleases (RGENs) repurposed from the type II clustered, regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) system are now widely used for genome editing in higher eukaryotic cells and whole organisms, revolutionising almost every discipline in biological research, medicine, and biotechnology. All of these nucleases, however, induce off-target mutations at sites homologous in sequence with on-target sites, limiting their utility in many applications including gene or cell therapy. In this review, we compare methods for detecting nuclease off-target mutations. We also review methods for profiling genome-wide off-target effects and discuss how to reduce or avoid off-target mutations.

• Mycobiology
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• 제42권4호
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• pp.322-330
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• 2014

The aim of this study was to identify and characterize new Flammulina velutipes laccases from its whole-genome sequence. Of the 15 putative laccase genes detected in the F. velutipes genome, four new laccase genes (fvLac-1, fvLac-2, fvLac3, and fvLac-4) were found to contain four complete copper-binding regions (ten histidine residues and one cysteine residue) and four cysteine residues involved in forming disulfide bridges, fvLac-1, fvLac-2, fvLac3, and fvLac-4, encoding proteins consisting of 516, 518, 515, and 533 amino acid residues, respectively. Potential N-glycosylation sites (Asn-Xaa-Ser/Thr) were identified in the cDNA sequence of fvLac-1 (Asn-454), fvLac-2 (Asn-437 and Asn-455), fvLac-3 (Asn-111 and Asn-237), and fvLac4 (Asn-402 and Asn-457). In addition, the first 19~20 amino acid residues of these proteins were predicted to comprise signal peptides. Laccase activity assays and reverse transcription polymerase chain reaction analyses clearly reveal that $CuSO_4$ affects the induction and the transcription level of these laccase genes.

• 미생물학회지
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• 제54권3호
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• pp.305-307
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• 2018

이 연구에서는 PacBio RS II 플랫폼을 사용하여 동해에서 분리된 해양 미생물 Pseudoalteromonas donghaensis $HJ51^T$의 전체 유전체 서열화를 수행하였다. 그 결과, 크기 3,646,857 bp, G + C 함량 41.8%인 염색체와 함께 크기 842,855 bp, G + C 함량 41.3% 및 크기 244,204 bp, G + C 함량 40.4%인 두 개의 플라스미드로 구성된 3개의 유전체 서열을 획득하였다. 이 유전체는 4,083개의 단백질 암호화 유전자와 127개의 RNA 유전자를 포함하고 있다. 다양한 생체 고분자 분해효소의 유전자원과 대장균과 유사한 세포외 단백질 분비 숙주로서의 개발에 이용될 수 있을 것으로 생각된다.

• Mycobiology
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• 제49권3호
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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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• 제63권1호
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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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• 제63권2호
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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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• 제66권1호
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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.

• 한국미생물·생명공학회지
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• 제46권3호
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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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• 제64권1호
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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.