• Journal of Microbiology and Biotechnology
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• v.23 no.4
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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.

• Research in Plant Disease
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• v.22 no.3
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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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• v.44 no.1
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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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• v.35 no.3
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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.

• Korean Journal of Plant Taxonomy
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• v.53 no.3
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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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• v.20 no.4
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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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• v.21 no.1
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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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• v.33 no.5
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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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• v.42 no.12
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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.

• Korean Journal of Microbiology
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• v.51 no.4
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• pp.329-337
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• 2015

All known genomes (N=10) in the order Nitrosomonadales were analyzed to contain 9,808 and 908 gene clusters in their pan-genome and core genome, respectively. Analyses with reference genomes belonging to other orders in Betaproteobacteria revealed that sizes of pan-genome and core genome were dependent on the number of genomes compared and the differences of genomes within a group. The sizes of pan-genomes of the genera Nitrosomonas and Nitrosospira were 7,180 and 4,586 and core genomes, 1,092 and 1,600, respectively, which implied that similarity of genomes in Nitrosospira were higher than Nitrosomonas. The genomes of Nitrosomonas contributed mostly to the size of the pan-genome and core genomes of Nitrosomonadales. COG analysis of gene clusters showed that the J (translation, ribosomal structure and biogenesis) category occupied the biggest proportions (9.7-21.0%) among COG categories in core genomes and its proportion increased in the group which genetic distances among members were high. The unclassified category (-) occupied very high proportions (34-51%) in pan-genomes. Ninety seven gene clusters existed only in Nitrosomonadales and not in reference genomes. The gene clusters contained ammonia monooxygenase (amoA and amoB) and -related genes (amoE and amoD) which were typical genes characterizing the order Nitrosomonadales while they contained significant amount (16-45%) of unclassified genes. Thus, these exclusively-conserved gene clusters might play an important role to reveal genetic specificity of the order Nitrosomonadales.