• 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.

• Journal of Genetic Medicine
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• v.7 no.2
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• pp.119-124
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• 2010

More than 7,000 rare Mendelian diseases have been reported, but less than half of all rare monogenic disorders has been discovered. In addition, the majority of mutations that are known to cause Mendelian disorders are located in protein-coding regions. Therefore, exome sequencing is an efficient strategy to selectively sequence the coding regions of the human genome to identify novel genes associated with rare genetic disorders. The "exome" represents all of the exons in the human genome, constituting about 1.5% of the human genome. Exome sequencing is carried out by targeted capture and intense parallel sequencing. After the first report of successful exome sequencing for the identification of causal genes and mutations in Freeman Sheldon syndrome, exome sequencing has become a standard approach to identify genes in rare Mendelian disorders. Exome sequencing is also used to search the causal genes and variants in complex diseases. The successful use of exome sequencing in Mendelian disorders and complex diseases will facilitate the development of personalized genomic medicine.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.54 no.6
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• pp.1045-1051
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• 2021

Eighty-nine different types of commercially salt-fermented fishery products comprising various raw materials were analyzed for total aerobic bacteria, number of coliform bacteria, fecal coliform, and Escherichia coli. The food-poisoning bacterial content of the samples was investigated using next-generation sequencing. The mean mass of total aerobic bacteria in Jeotgal was 6-1.8×10⁹ CFU/g, and that in Aekjeot and Sikhae was 4-2.2×10⁵ CFU/mL and 1.9×10⁵-8.4×10⁸ CFU/g, respectively. Coliform bacteria were detected in 9 (28.1%) of 32 Jeotgal samples; 15 (46.8%) of 32 seasonal Jeotgal samples; and in 5 (55.5%) of 9 Sikhae samples. Fecal coliform and E. coli were not detected in 86 of the 89 samples. Yersinia enterocolitica was detected only in Galchi jeot (salt-fermented hairtail) (1 type) and not in other Jeotgal samples. These results contribute to our knowledge regarding the bacterial stability of salt-fermented fishery products.

• KIPS Transactions on Computer and Communication Systems
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• v.8 no.10
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• pp.231-238
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• 2019

Analyzing next-generation genome sequencing data in a conventional way using single server may take several tens of hours depending on the data size. However, in order to cope with emergency situations where the results need to be known within a few hours, it is required to improve the performance of a single genome analysis. In this paper, we propose a parallelized method for pre-processing genome sequence data which can reduce the analysis time by utilizing the big data technology and the highperformance computing cluster which is connected to the high-speed network and shares the parallel file system. For the reliability of analytical data, we have chosen a strategy to parallelize the existing analytical tools and algorithms to the new environment. Parallelized processing, data distribution, and parallel merging techniques have been developed and performance improvements have been confirmed through experiments.

• Ocean and Polar Research
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• v.43 no.1
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• pp.45-51
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• 2021

Studies on marine zooplankton diversity and ecology are important for understanding marine ecosystem, as well as environmental conservation and fisheries management. DNA metabarcoding is known as a useful tool to reveal and understand diversity among animals, but a comparative evaluation with classical microscopy is still required in order to properly use it for marine zooplankton research. This study compared crustacean mesozooplankton taxa revealed by morphological analysis and metabarcoding of the cytochrome oxidase I (COI). A total of 17 crustacean species were identified by morphological analysis, and 18 species by metabarcoding. Copepods made up the highest proportion of taxa, accounting for more than 50% of the total number of species delineated by both methods. Cladocerans were not found by morphological analysis, whereas amphipods and mysids were not detected by metabarcoding. Unlike morphological analysis, metabarcoding was able to identify decapods down to the species level. There were some discrepancies in copepod species, which could be due to a lack of genetic database, or biases during DNA extraction, amplification, pooling and bioinformatics. Morphological analysis will be useful for ecological studies as it can classify and quantify the life history stages of marine zooplankton that metabarcoding cannot detect. Metabarcoding can be a powerful tool for determining marine zooplankton diversity, if its methods or database are further supplemented.

• Journal of Microbiology and Biotechnology
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• v.32 no.2
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• pp.149-159
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• 2022

Cancers of the lung and liver are the top 10 leading causes of cancer death worldwide. Thus, it is essential to identify the genes specifically expressed in these two cancer types to develop new therapeutics. Although many messenger RNA (mRNA) sequencing data related to these cancer cells are available due to the advancement of next-generation sequencing (NGS) technologies, optimized data processing methods need to be developed to identify the novel cancer-specific genes. Here, we conducted an analytical comparison between Bowtie2, a Burrows-Wheeler transform-based alignment tool, and Kallisto, which adopts pseudo alignment based on a transcriptome de Bruijn graph using mRNA sequencing data on normal cells and lung/liver cancer tissues. Before using cancer data, simulated mRNA sequencing reads were generated, and the high Transcripts Per Million (TPM) values were compared. mRNA sequencing reads data on lung/liver cancer cells were also extracted and quantified. While Kallisto could directly give the output in TPM values, Bowtie2 provided the counts. Thus, TPM values were calculated by processing the Sequence Alignment Map (SAM) file in R using package Rsubread and subsequently in python. The analysis of the simulated sequencing data revealed that Kallisto could detect more transcripts and had a higher overlap over Bowtie2. The evaluation of these two data processing methods using the known lung cancer biomarkers concludes that in standard settings without any dedicated quality control, Kallisto is more effective at producing faster and more accurate results than Bowtie2. Such conclusions were also drawn and confirmed with the known biomarkers specific to liver cancer.

• Journal of Environmental Science International
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• v.30 no.5
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• pp.379-389
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• 2021

Soil microorganism activity in an agricultural field is affected by various factors including climate conditions, soil chemical properties, and crop cultivation. In this study, we elucidate the correlation between microorganism activity and agricultural environment factors using the dehydrogenase activity (DHA) value, which is one of the indicators of soil microbial activity. As a result, the various factors noted above were related to the DHA value. Annual rainfall, soil Mg2+, bacterial and fungal diversities, types of crops, developmental stages, seasons, and cultivation status were highly correlated with the DHA value. Furthermore, next-generation sequencing (NGS) analysis was used to identify that the type of crop affected soil microbial compositions of both bacteria and fungi. Soil used for soybean cultivation showed the highest relative abundance for Verrucomicrobia, Planctomycetes, and Acidobacteria but Actinobacteria and Firmicutes had the lowest relative abundance. In the case of soil used for potato cultivation, Actinobacteria had the highest relative abundance but Proteobacteria had the lowest relative abundance. Armatimonadetes showed the highest relative abundance in soil used for cabbage cultivation. Among the fungal communities, Mortierellomycota had the highest relative abundance for soybean cultivation but the lowest relative abundance for cabbage cultivation; further, Rozellomycota, Chytridiomycota, and Cercozoa had the highest relative abundance for cabbage cultivation. Basidiomycota had the highest relative abundance for potato cultivation but the lowest relative abundance for soybean cultivation.

• The Korea Journal of Herbology
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• v.34 no.6
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• pp.91-97
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• 2019

Objective : To establish a reliable tool between for the distinction of original plants of Sanguisorbae Radix, we analyzed the complete chloroplast genome sequence of Sanguisorbae Radix and identified single nucleotide polymorphisms (SNPs). Materials and methods : The chloroplast genome sequence of Sanguisorba officinalis, Sanguisorba tenuifolia f. alba (Trautv. & Mey.) Kitam and Sanguisorba tenuifolia Fisch. ex Link obtained using next-generation sequencing technology were described and compared with those of other species to develop specific markers. Candidate genetic markers were identified to distinguish species from the chloroplast sequences of each species using Modified Phred Phrap Consed and CLC Genomics Workbench programs. Results : The structure of the chloroplast genome of each sample that had been assembled and verified was circular, and the length was about 155 kbp. Through comparative analysis of the chloroplast sequences, we found 220 nucleotides, 158 SNPs, and 62 Indel (insertion and/or deletion), to distinguish Sanguisorba officinalis, Sanguisorba tenuifolia f. alba (Trautv. & Mey.) Kitam and Sanguisorba tenuifolia Fisch. ex Link. Finally, 15 specific SNP genetic markers were selected for the verification at positions. Avaliable primers for the dried herb, which is used as medicine, were used to develop the PCR amplification product of Sanguisorbae Radix to assess the applicability of PCR analysis. Conclusion : In this study, we found that Fendel-qPCR analysis based on the chloroplast DNA sequences can be an efficient tool for discrimination of Sanguisorba officinalis, Sanguisorba tenuifolia f. alba (Trautv. & Mey.) Kitam and Sanguisorba tenuifolia Fisch. ex Link.

• Journal of Animal Science and Technology
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• v.63 no.6
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• pp.1423-1432
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• 2021

To elucidate the role and mechanism of microbes, we combined culture-dependent and culture-independent approaches to investigate differences in gut bacterial composition between sows and weaned pigs. Under anaerobic conditions, several nonselective and selective media were used for isolation from fecal samples. All isolated bacteria were identified and classified through 16S rRNA sequencing, and the microbiota composition of the fecal samples was analyzed by metagenomics using next generation sequencing (NGS) technology. A total of 278 and 149 colonies were acquired from the sow and weaned pig fecal samples, respectively. Culturomics analysis revealed that diverse bacterial genus and species belonged to Firmicutes, Actinobacteria, Proteobacteria, and Bacteroidetes were isolated from sow and weaned pigs. When comparing culture-dependent and culture-independent analyses, 191 bacterial species and 2 archaeal bacterial species were detected through culture-independent analysis, and a total of 23 bacteria were isolated through a culture-dependent approach, of which 65% were not detected by metagenomics. In conclusion, culturomics and metagenomics should be properly combined to fully understand the intestinal microbiota, and livestock-derived microbial resources should be informed by culturomic approaches to understand and utilize the mechanism of host-microbe interactions.

• Journal of Genetic Medicine
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• v.19 no.1
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• pp.14-21
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• 2022

Complex chromosome rearrangements (CCRs) are structural chromosomal rearrangements involving at least three chromosomes and more than two breakpoints. CCR carriers are generally phenotypically normal but related to higher risk of recurrent miscarriage and having abnormal offspring with congenital anomalies. However, most of CCR carriers are not aware of their condition until genetic analysis of either abortus or affected baby or parental karyotyping is performed. Herein, we present the case that CCR carrier patients can be identified by preimplantation genetic testing of preimplantation embryos. An infertile male patient with severe oligoasthenoteratozoospermia was diagnosed balanced reciprocal translocation, 46,XY,t(3;11) (p26;p14) at first. After attempting the first preimplantation genetic testing for structural rearrangement (PGT-SR) cycle, we found the recurrent segmental gain or loss on 21q21.3-q22.3 of five out of nine embryos. As a result of karyotype re-analysis, the patient's karyotype showed a balanced CCR involving chromosomes 3, 11, and 21 with three breakpoints 3p26, 11p14, and 21q21. The patient underwent two PGT-SR cycles, and a pregnancy was established after the transfer of an euploid embryo in the second cycle. Amniocentesis confirmed that the baby carried normal karyotype without mosaicism. At 37 weeks gestation, a healthy girl weighting 3,050 g was born.