• Korean Journal of Environmental Biology
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• v.30 no.2
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• pp.77-89
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• 2012

With the advent of the genomics era powered by DNA sequencing technologies, life science is being transformed significantly and biological research and development have been accelerated. Environmental biology concerns the relationships among living organisms and their natural environment, which constitute the global biogeochemical cycle. As sustainability of the ecosystems depends on biodiversity, examining the structure and dynamics of the biotic constituents and fully grasping their genetic and metabolic capabilities are pivotal. The high-speed high-throughput next-generation sequencing can be applied to barcoding organisms either thriving or endangered and to decoding the whole genome information. Furthermore, diversity and the full gene complement of a microbial community can be elucidated and monitored through metagenomic approaches. With regard to human welfare, microbiomes of various human habitats such as gut, skin, mouth, stomach, and vagina, have been and are being scrutinized. To keep pace with the rapid increase of the sequencing capacity, various bioinformatic algorithms and software tools that even utilize supercomputers and cloud computing are being developed for processing and storage of massive data sets. Environmental genomics will be the major force in understanding the structure and function of ecosystems in nature as well as preserving, remediating, and bioprospecting them.

• Journal of Microbiology and Biotechnology
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• v.29 no.12
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• pp.1957-1968
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• 2019

Tetraselmis is a green algal genus, some of whose species are important in aquaculture as well as biotechnology. In algal culture, fluorescent lamps, traditional light source for culturing algae, are now being replaced by a cost-effective light-emitting diodes (LEDs). In this study, we investigated the effect of LED light of different wavelengths (white, red, yellow, and blue) on the growth of Tetraselmis suecica and its associated microbial community structures using the next-generation sequencing (NGS). The fastest growth rate of T. suecica was shown in the red light, whereas the slowest was in yellow. The highest OTUs (3426) were identified on day 0, whereas the lowest ones (308) were found on day 15 under red light. The top 100 OTUs associated with day 0 and day 5 cultures of T. suecica under the red and yellow LED were compared. Only 26 OTUs were commonly identified among four samples. The highest numbers of unique OTUs were identified at day 0, indicating the high degree of initial microbial diversity of the T. suecica inoculum. The red light-unique OTUs occupied 34.98%, whereas the yellow-specific OTUs accounted for only 2.2%. This result suggested a higher degree of interaction in T. suecica culture under the red light, where stronger photosynthesis occurs. Apparently, the microbial community associated with T. suecica related to the oxygen produced by algal photosynthesis. This result may expand our knowledge about the algae-bacteria consortia, which would be useful for various biotechnological applications including wastewater treatment, bioremediation, and sustainable aquaculture.

• Journal of KIISE
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• v.42 no.12
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• pp.1584-1589
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• 2015

With the advancement of next-generation sequencing (NGS) technologies, various genome browsers have been introduced. Because existing browsers focus on comparison of the genomic data of extant species, however, there is a need for a genome browser for ancestral genomes and their evolution. In this paper, we introduce a genome browser, AGB (Ancestral Genome Browser), that displays ancestral genome data reconstructed from existing species. With AGB, it is possible to trace genomic variations that occurred during evolution in a simple and intuitive way. We explain the capability of AGB in terms of visualizing ancestral genomic information and evolutionary genomic variations. AGB is now available at http://bioinfo.konkuk.ac.kr/genomebrowser/.

• Korean Journal of Medicinal Crop Science
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• v.25 no.6
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• pp.411-417
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• 2017

Background: Adenophora triphylla var. japonica (Regel) H. Hara shows vegetative growth with radical leaves during the first year and shows reproductive growth with cauline leaves and bolting during the second year. In addition, the shape of the plant varies within the same species. For this reason, there are limitations to classifying the species by visual examination. However, there is not sufficient genetic information or molecular tools to analyze the genetic diversity of the plant. Methods and Results: Approximately 34.59 Gbp of raw data containing 342,487,502 reads was obtained from next generation sequencing (NGS) and these reads were assembled into 357,211 scaffolds. A total of 84,106 simple sequence repeat (SSR) regions were identified and 14,133 primer sets were designed. From the designed primer sets, 95 were randomly selected and were applied to the genomic DNA which was extracted from five plants and pooled. Thirty-nine primer sets showing more than two bands were finally selected as SSR markers, and were used for the genetic relationship analysis. Conclusions: The 39 novel SSR markers developed in this study could be used for the genetic diversity analysis, variety identification, new variety development and molecular breeding of A. triphylla.

• Food Science of Animal Resources
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• v.39 no.4
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• pp.585-600
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• 2019

Gouda cheese, one of most popular cheeses in the Korea, has been produced from only pasteurized milk in Korean dairy farms. Recently, it has become legally possible to produce ripened cheese manufactured with raw milk in Korea. In the present study, we investigated the physico-chemical and microbiological characteristics of Gouda cheese manufactured with raw (R-GC) or pasteurized milk (P-GC) during manufacturing and ripening. Particularly, this study characterized the bacterial community structure of two cheese types, which are produced without pasteurization during ripening based on next generation sequencing of 16S rRNA gene amplicons. During ripening, protein and fat content increased slightly, whereas moisture content decreased in both P-GC and R-GC. At the 6 wk of ripening, R-GC became softer and smoother and hence, the values of hardness and gumminess, chewiness in R-GC was lower than that of P-GC. Metagenomic analysis revealed that the bacterial genera used a starter cultures, namely Lactococcus and Leuconostoc were predominant in both P-GC and R-GC. Moreover, in R-GC, the proportion of coliform bacteria such as Escherichia, Leclercia, Raoultella, and Pseudomonas were detected initially but not during ripening. Taken together, our finding indicates the potential of manufacturing with Gouda cheese from raw milk and the benefits of next generation sequencing for microbial community composition during cheese ripening.

• Korean Journal of Clinical Laboratory Science
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• v.55 no.3
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• pp.203-212
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• 2023

Since the coronavirus disease-2019 (COVID-19) outbreak, it has been generally believed that a medical technologists (MTs) are supposed to perform polymerase chain reaction tests and next-generation sequencing (NGS) in the hospitals. However, many do not recognize that the duty of MT for clinical genetic testing has not been stated in the Medical Laws (72.5% for MT, N=200; 62.8% for students, N=123). In this regard, to evaluate the feasibility of MT's role for NGS genetic testing, we requested our subjects to fill out an online survey and analyzed the data. Among them, it shows that the scope of MT's role, including NGS performance should include clinical genetic testing (99.5% for MT, N=200; 86.8% for students, N=123). Also, questions on clinical genetics, which is associated with both cellular genetics and molecular genetic questions should be included in the National MT License Problem Bank (97.5% for MT; 71.4% for students). Based on these results, the Korean Association of Medical Technologists needs to cooperate synergically with the Academic Association of Biomedical Laboratory Science with respect to genetic education and legislation for the future benefit of both MTs and students.

• Journal of Conservation Science
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• v.37 no.4
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• pp.357-361
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• 2021

In order to determine the changes in microbial community due to termites, soil microorganisms surrounding the termites were investigated. First, bacterial communities from soil with termites collected at Seonamsa temple, Suncheon city, Korea were compared by next-generation sequencing (NGS, Illumina Miseq). The bacterial composition of soil from Daeungjeon without termites and the soil from Josadang, Palsangjeon, and Samjeon with termites were compared. Next, the bacterial composition of these soils was also compared with that of humus soil cultured with termites. A total high-quality sequences of 71,942 and 72,429 reads were identified in Seonamsa temple's soil and humus soil, respectively. The dominant phyla in the collected Seonamsa temple's soil were Proteobacteria (27%), Firmicutes (24%) and Actinobacteria (21%), whereas those in the humus soil were Bacteriodetes (56%) and Proteobacteria (37%). Using a two-dimensional plot to explain the principal coordinate analysis of operational taxonomic unit compositions of the soil samples, it was confirmed that the samples were divided into soil with and without termites, and it was especially confirmed that the Proteobacteria phylum was increased in humus soil with termites than in humus soil without termites.

• Korean Journal of Plant Taxonomy
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• v.53 no.3
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• pp.181-200
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• 2023

Owing to the rapid development of sequencing technologies, more than 1,000 plant genomes have been sequenced and released. Among them, 69 Korean plant taxa (85 genome sequences) contain at least one whole-genome sequence despite the fact that some samples were not collected in Korea. The sequencing-by-synthesis method (next-generation sequencing) and the PacBio (third-generation sequencing) method were the most commonly used in studies appearing in 65 publications. Several scaffolding methods, such as the Hi-C and 10x types, have also been used for pseudo-chromosomal assembly. The most abundant families among the 69 taxa are Rosaceae (10 taxa), Brassicaceae (7 taxa), Fabaceae (7 taxa), and Poaceae (7 taxa). Due to the rapid release of plant genomes, it is necessary to assemble the current understanding of Korean plant species not only to understand their whole genomes as our own plant resources but also to establish new tools for utilizing plant resources efficiently with various analysis pipelines, including AI-based engines.

• Journal of Life Science
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• v.25 no.3
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• pp.349-356
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• 2015

Thanks to recent advances in next-generation sequencing (NGS) technology, diverse livestock species have been dissected at the genome-wide sequence level. As for cattle, there are currently four Korean indigenous breeds registered with the Domestic Animal Diversity Information System of the Food and Agricultural Organization of the United Nations: Hanwoo, Chikso, Heugu, and Jeju Heugu. These native genetic resources were recently whole-genome resequenced using various NGS technologies, providing enormous single nucleotide polymorphism information across the genomes. The NGS application further provided biological such that Korean native cattle are genetically distant from some cattle breeds of European origins. In addition, the NGS technology was successfully applied to detect structural variations, particularly copy number variations that were usually difficult to identify at the genome-wide level with reasonable accuracy. Despite the success, those recent studies also showed an inherent limitation in sequencing only a representative individual of each breed. To elucidate the biological implications of the sequenced data, further confirmatory studies should be followed by sequencing or validating the population of each breed. Because NGS sequencing prices have consistently dropped, various population genomic theories can now be applied to the sequencing data obtained from the population of each breed of interest. There are still few such population studies available for the Korean native cattle breeds, but this situation will soon be improved with the recent initiative for NGS sequencing of diverse native livestock resources, including the Korean native cattle breeds.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.58-58
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• 2017

The advent of next generation sequencing technology has elicited plenty of sequencing data available in agriculturally relevant plant species. For most crop species, it is too expensive to obtain the whole genome sequence data with sufficient coverage. Thus, many approaches have been developed to bring down the cost of NGS. Genotyping-by-sequencing (GBS) is a cost-effective genotyping method for complex genetic populations. GBS can be used for the analysis of genomic selection (GS), genome-wide association study (GWAS) and constructing haplotype and genetic linkage maps in a variety of plant species. For efficiently dealing with plant GBS data, the TASSEL-GBS pipeline is one of the most popular choices for many researchers. TASSEL-GBS is JAVA based a software package to obtain genotyping data from raw GBS sequences. Here, we describe application of GBS and bioinformatics pipeline of TASSEL-GBS for analyzing plant genetics data.