• 한국미생물·생명공학회지
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• 제51권4호
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• pp.562-565
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• 2023

Escherichia coli-specific phage, KFS-EC1, was isolated and purified from a slaughterhouse. The complete genome of the phage was obtained using Illumina MiSeq platforms. Its assembled genome consisted of a single chromosome of 164,715 bp with a GC content of 40.5%. The phage genome contained 170 hypothetical and 101 functional ORFs, and exhibited orthologous average nucleotide identity values of >95% with other E. coli phages belonging to the family Straboviridae. Additionally, phylogenetic analysis revealed that KFS-EC1 was finally classified into the family Straboviridae of the genus Caudoviricetes. The genome has been deposited in GenBank under the accession number NC_055757.1.

• Journal of Ginseng Research
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• 제40권2호
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• pp.127-134
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• 2016

Background: Rhizospheric fungi play an essential role in the plantesoil ecosystem, affecting plant growth and health. In this study, we evaluated the fungal diversity in the rhizosphere soil of 2-yr-old healthy Panax notoginseng cultivated in Wenshan, China. Methods: Culture-independent Illumina MiSeq and culture-dependent techniques, combining molecular and morphological characteristics, were used to analyze the rhizospheric fungal diversity. A diffusion test was used to challenge the phytopathogens of P. notoginseng. Results: A total of 16,130 paired-end reads of the nuclear ribosomal internal transcribed spacer 2 were generated and clustered into 860 operational taxonomic units at 97% sequence similarity. All the operational taxonomic units were assigned to five phyla and 79 genera. Zygomycota (46.2%) and Ascomycota (37.8%) were the dominant taxa; Mortierella and unclassified Mortierellales accounted for a large proportion (44.9%) at genus level. The relative abundance of Fusarium and Phoma sequenceswas high, accounting for 12.9% and 5.5%, respectively. In total,113 fungal isolates were isolated from rhizosphere soil. They were assigned to five classes, eight orders (except for an Incertae sedis), 26 genera, and 43 species based on morphological characteristics and phylogenetic analysis of the internal transcribed spacer. Fusarium was the most isolated genus with six species (24 isolates, 21.2%). The abundance of Phoma was also relatively high (8.0%). Thirteen isolates displayed antimicrobial activity against at least one test fungus. Conclusion: Our results suggest that diverse fungi including potential pathogenic ones exist in the rhizosphere soil of 2-yr-old P. notoginseng and that antagonistic isolates may be useful for biological control of pathogens.

• 대한수혈학회지
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• 제29권3호
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• pp.310-319
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• 2018

배경: 최근 차세대염기서열분석법(Next Generation Sequencing: NGS)을 이용한 HLA 형별 분석에 대한 연구가 활발히 진행되고 있다. 이에 HLA 고해상도 분석법의 내재적 한계인 위상 모호성의 문제를 해결하고, 대량 검체 처리가 가능한 NGS 기반 고해상도 HLA 형별 검사법을, 자체 기술로 개발하고자 본 연구를 실시하였다. 방법: HLA NGS를 위한 핵산 추출 조건, 라이브러리 제작 및 PCR 체계 확립, 그리고 생물정보학을 이용한 HLA 형별 분석법을 개발하였다. 본 기관에서 개발한 NGS 기반 HLA 형별 검사의 정확성을 알아보기 위해 SSOP법으로 HLA 형별을 알고 있는 192개 검체와 SBT법으로 HLA 형별을 알고 있는 28개 검체에 대해 NGS 기반으로 검사한 HLA-A, -B 그리고 -DR 형별 결과를 비교해 보았다. 결과: 두 단계의 PCR을 통한 DNA 라이브러리 제작과 MiSeq (Illumina Inc., San Diego, USA) 기기를 이용한 NGS 시퀸싱 그리고 데이터 분석 시스템을 구축하였다. 기존에 HLA 형별을 알고 있는 220개 혈액 검체에 대해 NGS 기반 HLA 형별검사 결과가 모두 일치함을 확인하였다. 결론: NSG 기반 HLA 형별 검사법은 많은 검체를 효율적인 시간 내에 처리가 가능하여 조혈모세포기증 희망자 HLA 검사 등에 유용할 것으로 기대된다.

• 한국미생물·생명공학회지
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• 제51권3호
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• pp.289-292
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• 2023

Thermotolerant Bacillus subtilis NIB353 was isolated from Nuruk, a traditional Korean fermentation starter. The complete B. subtilis NIB353 genome sequence was obtained using MinION and Illumina (MiSeq) platforms. The B. subtilis NIB353 genome sequence was 4,247,447 bp with a GC content of 43%. The B. subtilis NIB353 strain exhibited orthologous average nucleotide identity values of 98.39% and 98.38% with B. subtilis 168 and B. subtilis ATCC6051a, respectively. The genome has been deposited in GenBank under the accession number NZ_CP089148.1.

• 한국자원식물학회:학술대회논문집
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• 한국자원식물학회 2019년도 추계학술대회
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• pp.73-73
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• 2019

Angelica gigas Nakai (Korean danggui), a member of the Umbelliferae family, is a Korean traditional medicinal plant whose roots have been used for treating gynecological diseases. Transcriptomics is the study of the transcriptome, which is the complete set of RNA transcripts that are produced by the genome, using high-throughput methods, such as microarray analysis. In this study, transcriptome analysis of A.gigas Nakai was carried out. Transcriptome sequencing and assembly was carried out by using Illumina Hiseq 2500, Velvet and Oases. A total of 109,591,555 clean reads of A. gigas Nakai was obtained after trimming adaptors. The obtained reads were assembled with an average length of 1,154 bp, a maximum length of 13,166 bp, a minimum length of 200 pb, and N50 of 1,635 bp. Functional annotation and classification was performed using NCBI NR, InterprotScan, KOG, KEGG and GO. Candidate genes for phenylpropanoid biosynthesis were obtanied from A.gigas transcriptome and the genes and its proteins were confirmed through the NCBI homology BLAST searches, revealing high identity with other othologous genes and proteins from various plants pecies. In RNA sequencing analysis using an Illumina Next-Seq2500 sequencer, we identified a total 94,930 transcripts and annotated 71,281 transcripts, which provide basic information for further research in A.gigas Nakai. Our transcriptome data reveal that several differentially expressed genes related to flower color in A.gigas Nakai. The results of this research provide comprehensive information on the A.gigas Nakai genome and enhance our understanding of the flower color related gene pathways in this plant.

• 한국미생물·생명공학회지
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• 제49권2호
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• pp.225-238
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• 2021

옥수수(Zea mays)와 톨페스큐(Festuca arundinacea) 근권 토양을 접종원으로 사용하여 농화배양을 통해 CH₄ 산화컨소시움과 N₂O 환원 컨소시움을 얻었다. Illumina MiSeq 염기서열 분석법으로 접종원과 컨소시움의 세균 군집 특성을 비교하였고, 컨소시움의 CH₄ 산화와 N₂O 환원 활성에 미치는 뿌리삼출물의 영향을 규명하였다. 접종원이 다름에도 불구하고 옥수수와 톨페스큐 유래 CH₄ 산화 컨소시움 사이의 유사성이 높았고, 2종의 N₂O 환원 컨소시움도 서로 유사성이 높았다. 2종의 CH₄ 산화 컨소시움에서 우점도가 높은 metanotrophs는 Methylosarcina, Methylococcus 및 Methylocystis이었다. 2 종의 N₂O 환원 컨소시움에서 대표적인 N₂O 환원 세균은 Cloacibacterium, Azonexus 및 Klebsiella이었다. 옥수수 근권 유래 N₂O 환원 컨소시움의 N₂O 환원 속도는 옥수수 뿌리삼출물 첨가에 의해 1.6배, 톨페스큐 유래 컨소시움의 N₂O 환원 속도는 톨페스큐 뿌리삼출물 첨가에 의해 2.7배 향상되었다. 그러나 CH₄ 산화 컨소시움의 활성은 뿌리삼출물 첨가에 의해 향상되지 않았다. 본 연구의 옥수수 및 톨페스큐 근권 유래 CH₄ 산화 및 N₂O 환원 컨소시움은 유류 오염 정화과정에서 non-CO₂ 온실가스배출을 저감하는데 활용 가능하다.

• 식물분류학회지
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• 제50권3호
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• pp.327-332
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• 2020

Microsatellite markers were developed as a tool for phylogeographic studies of Hosta capitata. We also assessed cross-amplification in species closely related to Hosta capitata. We produced 28 polymorphic microsatellite markers by mapping 300 bp paired-end reads obtained from Illumina MiSeq data of H. capitata. In H. capitata, the number of alleles per locus ranged from 1 to 13. Observed and expected heterozygosity ranged from 0.000 to 0.844 and 0.000 to 0.832, respectively. Additionally, 13 loci were successfully transferable to the related species of H. minor and H. venusta. These markers will provide a powerful genetic tool not only for elucidating the phylogeographic patterns of H. capitata populations but also for studying the genetic delimitation of H. capitata from its related species.

• 한국축산식품학회지
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• 제37권4호
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• pp.535-541
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• 2017

This study investigated the psychrotrophic bacteria isolated from chicken meat to characterize their microbial composition during refrigerated storage. The bacterial community was identified by the Illumina MiSeq method based on bacterial DNA extracted from spoiled chicken meat. Molecular identification of the isolated psychrotrophic bacteria was carried out using 16S rDNA sequencing and their putrefactive potential was investigated by the growth at low temperature as well as their proteolytic activities in chicken meat. From the Illumina sequencing, a total of 187,671 reads were obtained from 12 chicken samples. Regardless of the type of chicken meat (i.e., whole meat and chicken breast) and storage temperatures ($4^{\circ}C$ and $10^{\circ}C$), Pseudomonas weihenstephanensis and Pseudomonas congelans were the most prominent bacterial species. Serratia spp. and Acinetobacter spp. were prominent in chicken breast and whole chicken meat, respectively. The 118 isolated strains of psychrotrophic bacteria comprised Pseudomonas spp. (58.48%), Serratia spp. (10.17%), and Morganella spp. (6.78%). All isolates grew well at $10^{\circ}C$ and they induced different proteolytic activities depending on the species and strains. Parallel analysis of the next generation sequencing and culture dependent approach provides in-depth information on the biodiversity of the spoilage microbiota in chicken meat. Further study is needed to develop better preservation methods against these spoilage bacteria.

• Journal of Microbiology and Biotechnology
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• 제33권8호
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• pp.1013-1022
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• 2023

Arbuscular mycorrhizal fungi (AMF) are widespread soil endophytic fungi, forming mutualistic relationships with the vast majority of land plants. Biochar (BC) has been reported to improve soil fertility and promote plant growth. However, limited studies are available concerning the combined effects of AMF and BC on soil community structure and plant growth. In this work, a pot experiment was designed to investigate the effects of AMF and BC on the rhizosphere microbial community of Allium fistulosum L. Using Illumina high-throughput sequencing, we showed that inoculation of AMF and BC had a significant impact on soil microbial community composition, diversity, and versatility. Increases were observed in both plant growth (the plant height by 8.6%, shoot fresh weight by 12.1%) and root morphological traits (average diameter by 20.5%). The phylogenetic tree also showed differences in the fungal community composition in A. fistulosum. In addition, Linear discriminant analysis (LDA) effect size (LEfSe) analysis revealed that 16 biomarkers were detected in the control (CK) and AMF treatment, while only 3 were detected in the AMF + BC treatment. Molecular ecological network analysis showed that the AMF + BC treatment group had a more complex network of fungal communities, as evidenced by higher average connectivity. The functional composition spectrum showed significant differences in the functional distribution of soil microbial communities among different fungal genera. The structural equation model (SEM) confirmed that AMF could improve the microbial multifunctionality by regulating the rhizosphere fungal diversity and soil properties. Our findings provide new information on the effects of AMF and biochar on plants and soil microbial communities.

• 한국자원식물학회:학술대회논문집
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• 한국자원식물학회 2018년도 춘계학술발표회
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• pp.37-37
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• 2018

The genus Crepidiastrum (Asteraceae), containing ca. 20 species, is mainly distributed in Asia. Crepidiastrum denticulatum, an edible plant that commonly call "e-go-deulppae-gi" in Korean, distributes in Korea, Japan, and China. The complete chloroplast (cp) genome sequences of C. denticulatum was characterized from MiSeq2000 (Illumina Co.) pair-end sequencing data. The cp genome of C. denticulatum has a total sequence length of 152,689 bp and show a typical quadripartite structure. It consists of the large single copy (LSC: 84,022 bp), small single copy (SSC: 18,519 bp), separated by a pair of inverted repeats (IRs: 25,074 bp) and contains 110 unique genes and 18 genes duplicated in the IR regions. Our comparative analysis identified three cpDNA regions (matK, rbcL, and psbA-trnH) from three Crepidiastrum species, which may be useful for molecular identification of each species, and providing a guideline for its clear confirming about dried medical herb.