• Journal of Microbiology and Biotechnology
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• 제23권4호
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• pp.459-466
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• 2013

The lactic acid bacterium Streptococcus thermophilus is widely used as a starter culture for the production of dairy products. Whole-genome sequencing is expected to utilize the genetic basis behind the metabolic functioning of lactic acid bacterium (LAB), for development of their use in biotechnological and probiotic applications. We sequenced the whole genome of Streptococcus thermophilus MTCC 5461, the strain isolated from a curd source, by 454 GS-FLX titanium and Ion Torrent PGM. We performed comparative genome analysis using the local BLAST and RDP for 16S rDNA comparison and by the RAST server for functional comparison against the published genome sequence of Streptococcus thermophilus CNRZ 1066. The whole genome size of S. thermophilus MTCC 5461 is of 1.73Mb size with a GC content of 39.3%. Streptococcal virulence-related genes are either inactivated or absent in the strain. The genome possesses coding sequences for features important for a probiotic organism such as adhesion, acid tolerance, bacteriocin production, and lactose utilization, which was found to be conserved among the strains MTCC 5461 and CNRZ 1066. Biochemical analysis revealed the utilization of 17 sugars by the bacterium, where the presence of genes encoding enzymes involved in metabolism for 16 of these 17 sugars were confirmed in the genome. This study supports the facts that the strain MTCC 5461 is nonpathogenic and harbors essential features that can be exploited for its probiotic potential.

• 식물병연구
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• 제22권3호
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• pp.194-197
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• 2016

Chinese yam necrotic mosaic virus (CYNMV) is one of the most widespread viruses in Chinese yam (Dioscorea opposita Thunb.) and causes serious yield losses. Currently, genetic information of CYNMV is very restricted and complete genome sequences of only two isolates (one from Japan and another from China) have been reported. In this study, we determined complete genome sequence of the CYNMV isolate AD collected from Andong, Korea. Genetic analysis of the polyprotein amino acid sequence revealed that the Korean isolate AD has high similarity with the Japanese isolate PES3 (97%) but relatively low similarity with the Chinese isolate FX1 (78%). Phylogenetic analysis using the CYNMV 3' proximal nucleotide sequences harboring the coat protein and 3' untranslated region further supported genetic relationship among the CYNMV isolates. Based on comparative analysis of the CYNMV genome sequences determined in this study and other previous studies, we generated molecular detection primers that are highly specific and efficient for CYNMV diagnosis.

• Journal of Ginseng Research
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• 제44권1호
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• pp.135-144
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• 2020

Background: Panax species are important herbal medicinal plants in the Araliaceae family. Recently, we reported the complete chloroplast genomes and 45S nuclear ribosomal DNA sequences from seven Panax species, two (P. quinquefolius and P. trifolius) from North America and five (P. ginseng, P. notoginseng, P. japonicus, P. vietnamensis, and P. stipuleanatus) from Asia. Methods: We conducted phylogenetic analysis of these chloroplast sequences with 12 other Araliaceae species and comprehensive comparative analysis among the seven Panax whole chloroplast genomes. Results: We identified 1,128 single nucleotide polymorphisms (SNP) in coding gene sequences, distributed among 72 of the 79 protein-coding genes in the chloroplast genomes of the seven Panax species. The other seven genes (including psaJ, psbN, rpl23, psbF, psbL, rps18, and rps7) were identical among the Panax species. We also discovered that 12 large chloroplast genome fragments were transferred into the mitochondrial genome based on sharing of more than 90% sequence similarity. The total size of transferred fragments was 60,331 bp, corresponding to approximately 38.6% of chloroplast genome. We developed 18 SNP markers from the chloroplast genic coding sequence regions that were not similar to regions in the mitochondrial genome. These markers included two or three species-specific markers for each species and can be used to authenticate all the seven Panax species from the others. Conclusion: The comparative analysis of chloroplast genomes from seven Panax species elucidated their genetic diversity and evolutionary relationships, and 18 species-specific markers were able to discriminate among these species, thereby furthering efforts to protect the ginseng industry from economically motivated adulteration.

• Bulletin of the Korean Chemical Society
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• 제35권3호
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• pp.933-937
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• 2014

A derivative of Mycobacterium bovis Bacillus Calmette-Guerin (BCG) has been used for the preparation of tuberculosis vaccines. To establish a Korean tuberculosis vaccine derived from BCG-Pasteur $1173P_2$, genome sequencing of a BCG-Korea strain was completed by Joung and coworkers. A comparison analysis of the genome sequences of the BCG-Pasteur $1173P_2$ and BCG-Korea strains showed marginal increases in the total genome length (~0.05%) and the number of genes (~4%) in the BCG-Korea genome. However, how the genomic changes affect the BCG-Korea protein expression levels remains unknown. Here, we provide evidence of the proteomic alterations in the BCG-Korea strain by using a SWATH-based mass spectrometric approach (Sequential Window Acquisition of all THeoretical mass spectra). Twenty BCG proteins were selected by top-rank identification in the BCG proteome analysis and the proteins were quantified by the SWATH method. Thirteen of 20 proteins showing significant changes were enough to discriminate between the two BCG proteomes. The SWATH method is very straightforward and provides a promising approach owing to its strong reliability and reproducibility during the proteomic analysis.

• 식물분류학회지
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• 제53권3호
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• pp.237-241
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• 2023

The genus Scrophularia L. (Scrophulariaceae) comprises 200-270 species worldwide and is a taxonomically challenging lineage, displaying morphological diversity and hybridization. S. kakudensis is morphologically similar to the closely related taxa S. kakudensis var. microphylla, S. pilosa, and S. cephalantha. Therefore, the purpose of this study was to sequence the chloroplast (cp) genome of S. kakudensis using next-generation sequencing and compare it to those of related taxa. The complete cp genome sequence of Scrophularia kakudensis was found to be 152,355 bp long, consisting of a pair of inverted repeats of 25,485 bp that separate a large single-copy (LSC) of 83,479 bp from small single-copy regions of 17,909 bp. The cp genome contained 78 protein-coding genes, 30 tRNAs, and four rRNAs. A phylogenetic analysis based on 78 protein-coding genes from six Scrophularia species showed S. kakudensis and S. cephalantha formed with 100% bootstrap values. We compared the complete cp genomes of S. kakudensis and S. cephalantha and identified seven sequence divergence regions: matK/rps16, rps16/trnQ, trnS/trnG, rpoB/trnC, trnS/trnG, rpl32/trnL, and ndhD/psaC. These regions may be useful for determining the phylogenetic relationships among S. kakudensis-related species.

• Genomics & Informatics
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• 제20권4호
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• pp.43.1-43.18
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• 2022

Atropa belladonna is a valuable medicinal plant and a commercial source of tropane alkaloids, which are frequently utilized in therapeutic practice. In this study, bioinformatic methodologies were used to examine the pattern of coding sequences and the factors that might influence codon usage bias in the chloroplast genome of Atropa belladonna and other nightshade genomes. The chloroplast engineering being a promising field in modern biotechnology, the characterization of chloroplast genome is very important. The results revealed that the chloroplast genomes of Nicotiana tabacum, Solanum lycopersicum, Capsicum frutescens, Datura stramonium, Lyciumbarbarum, Solanum melongena, and Solanum tuberosum exhibited comparable codon usage patterns. In these chloroplast genomes, we observed a weak codon usage bias. According to the correspondence analysis, the genesis of the codon use bias in these chloroplast genes might be explained by natural selection, directed mutational pressure, and other factors. GC12 and GC3S were shown to have no meaningful relationship. Further research revealed that natural selection primarily shaped the codon usage in A. belladonna and other nightshade genomes for translational efficiency. The sequencing properties of these chloroplast genomes were also investigated by investing the occurrences of palindromes and inverted repeats, which would be useful for future research on medicinal plants.

• Journal of Veterinary Science
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• 제21권1호
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• pp.11.1-11.7
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• 2020

The increase in canine skin and soft tissue infections, such as pyoderma and otitis, caused by Staphylococcus schleiferi strains, is of significant zoonotic concern. In this study, we report the first complete genome sequence for a methicillin-resistant clinical isolate of S. schleiferi (MRSS) designated as SS4, obtained from a dog with otitis externa, in Korea. The genome of SS4 strain was of 2,539,409 bp and presented high G+C content ratio (35.90%) with no plasmid. Comparative analysis of SS4 genome revealed that it is closely related to 2142-05 and 5909-02 strains isolated from the canine skin infections in the USA.

• Journal of Microbiology and Biotechnology
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• 제33권5호
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• pp.644-655
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• 2023

Safety assessment and functional analysis of probiotic candidates are important for their industrial applications. Lactiplantibacillus plantarum is one of the most widely recognized probiotic strains. In this study we aimed to determine the functional genes of L. plantarum LRCC5310, isolated from kimchi, using next-generation, whole-genome sequencing analysis. Genes were annotated using the Rapid Annotations using Subsystems Technology (RAST) server and the National Center for Biotechnology Information (NCBI) pipelines to establish the strain's probiotic potential. Phylogenetic analysis of L. plantarum LRCC5310 and related strains showed that LRCC5310 belonged to L. plantarum. However, comparative analysis revealed genetic differences between L. plantarum strains. Carbon metabolic pathway analysis based on the Kyoto Encyclopedia of Genes and Genomes database showed that L. plantarum LRCC5310 is a homofermentative bacterium. Furthermore, gene annotation results indicated that the L. plantarum LRCC5310 genome encodes an almost complete vitamin B₆ biosynthetic pathway. Among five L. plantarum strains, including L. plantarum ATCC 14917^T , L. plantarum LRCC5310 detected the highest concentration of pyridoxal 5'-phosphate with 88.08 ± 0.67 nM in MRS broth. These results indicated that L. plantarum LRCC5310 could be used as a functional probiotic for vitamin B₆ supplementation.

• BMB Reports
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• 제42권12호
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• pp.823-828
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• 2009

Techniques for analyzing protein-DNA interactions on a genome-wide scale have recently established regulatory roles for distal enhancers. However, the large sizes of higher eukaryotic genomes have made identification of these elements difficult. Information regarding sequence conservation, exon annotation and repetitive regions can be used to reduce the size of the search region. However, previously developed resources are inadequate for consolidating such information. CONVIRT is a web resource for the identification of transcription factor binding sites and also features comparative genomics. Genomic information on ortholog-independent conserved regions, exons, repeats and sequences is integrated into the virtual chromosome, and statistically over-represented single or combinations of transcription factor binding sites are sought. CONVIRT provides regulatory network analysis for several organisms with long promoter regions and permits inter-species genome alignments. CONVIRT is freely available at http://biosoft.kaist.ac.kr/convirt.

• 미생물학회지
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• 제51권4호
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• pp.329-337
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• 2015

Nitrosomonadales 목에서 속하는 균주 중 현재 유전체 서열이 알려진 모든 유전체(N=10)를 이용하여 범유전체 및 핵심유전체 분석을 수행한 결과, 각각 9,808개와 908개 유전자클러스터를 포함하는 것을 확인하였다. Betaproteobacteria의 다른 목의 참조군들과 비교를 통하여 범유전체와 핵심유전체의 크기에 유전체의 수와 집단 내의 유전체들의 차이가 영향을 미치는 것을 확인하였다. Nitrosomonas 속과 Nitrosospira 속의 범유전체는 7,180개와 4,586개, 핵심유전체는 1,092개와 1,600로로 각각 측정되어 Nitrosospira 속의 동질성이 더 높은 것을 확인하였다. Nitrosomonadales 목의 범유전체와 핵심유전체의 크기에 Nitrosomonas 속이 대부분의 영향을 미치는 것을 확인하였다. COG 분석을 통하여 핵심유전체의 크기에는 J (translation, ribosomal structure and biogenesis) 범주가 가장 큰 비율(9.7-21.0%)을 차지하며, 유전체 사이의 유전적 거리가 먼 집단일수록 그 비율이 높아지는 것을 확인하였다. 범유전체의 크기에는 "-" (unclassified) 범주가 34-51%의 높은 비율을 차지하고 있을 정도로 큰 영향을 미치는 것을 확인하였다. 총 97개의 유전자 클러스터가 참조군에는 없고 Nitrosomonadales에만 존재하는 것을 확인하였다. 이들 클러스터들은 Nitrosomonadales을 특징 지우는 유전자들인 ammonia monooxygenase의 유전자인 amoA와 amoB와 그와 관련 있는 amoE와 amoD들을 포함하는 반면에 unclassified 유전자들도 상당량(16-45%)을 포함하고 있다. 이러한 유전자 클러스터는 Nitrosomonadales의 유전적 특이성을 밝히는 데 중요한 역할을 할 것이다.