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

• Clinical and Experimental Pediatrics
• /
• v.53 no.3
• /
• pp.397-407
• /
• 2010

Purpose : The F9 gene is known to be the causative gene for hemophilia B, but unfortunately the detection rate for restriction fragment length polymorphism-based linkage analysis is only 55.6%. Direct DNA sequencing can detect 98% of mutations, but this alternative procedure is very costly. Here, we conducted multiplex polymerase chain reactions (PCRs) and conformation sensitive gel electrophoresis (CSGE) to perform a screened DNA sequencing for the F9 gene, and we compared the results with direct sequencing in terms of accuracy, cost, simplicity, and time consumption. Methods : A total of 27 unrelated hemophilia B patients were enrolled. Direct DNA sequencing was performed for 27 patients by a separate institute, and multiplex PCR-CSGE screened sequencing was done in our laboratory. Results of the direct DNA sequencing were used as a reference, to which the results of the multiplex PCR-CSGE screened sequencing were compared. For the patients whose mutation was not detected by the 2 methods, multiplex ligation-dependent probe amplification (MLPA) was conducted. Results : With direct sequencing, the mutations could be identified from 26 patients (96.3%), whereas for multiplex PCRCSGE screened sequencing, the mutations could be detected in 23 (85.2%). One patient's mutation was identified by MLPA. A total of 21 different mutations were found among the 27 patients. Conclusion : Multiplex PCR-CSGE screened DNA sequencing detected 88.9% of mutations and reduced costs by 55.7% compared with direct DNA sequencing. However, it was more labor-intensive and time-consuming.

• International Journal of Oral Biology
• /
• v.45 no.3
• /
• pp.77-83
• /
• 2020

In the oral cavity, complex microbial community is shaped by various host and environmental factors. Extensive literature describing the oral microbiome in the context of oral health and disease is available. Advances in DNA sequencing technologies and data analysis have drastically improved the analysis of the oral microbiome. For microbiome study, bacterial 16S ribosomal RNA gene amplification and sequencing is often employed owing to the cost-effective and fast nature of the method. In this review, practical considerations for performing a microbiome study, including experimental design, molecular analysis technology, and general data analysis, will be discussed.

• Mycobiology
• /
• v.32 no.3
• /
• pp.119-122
• /
• 2004

The intergenic spacer(IGS) sequence of Fusarium oxysporum have been reported to provide reliable information concerning intraspecific variation and phylogeny of fungal species. The eleven strains of Fusarium oxysporum and its formae speciales belonging to section Elegans were compared with sequencing analysis. The direct sequencing of partial IGS was carried out using PCR with primer NIGS1(5'-CTTCGCCTCGATTTCCCCAA-3')/NIGS2(5'-TCGTCGCCGACAGTTTTCTG-3') and internal primer NIGS3(5'-TCGAGGATCGATTCGAGG-3')/NIGS4(5'-CCTCGAATCGATCCTCGA-3'). A single PCR product was found for each strain. The PCR fragments were sequenced and revealed a few within species polymorphisms at the sequence level. The size of partial IGS sequencing of F. oxysporum was divided into three groups; $526{\sim}527$ bp including F. o. f. sp. chrysanthemi, cucumerinum, cyclaminis, lycopersici, and fragariae; $514{\sim}516$ bp including F. o. f. sp. lilii, conglutinans, and raphani; 435 bp for F. o. f. sp. cucumerinum from Korea. Sequence analysis of PCR products showed that transitions were more frequent than transversions as well as the average numbers of substitution per site were range 0.41% to 3.54%.

• Genomics & Informatics
• /
• v.13 no.4
• /
• pp.119-125
• /
• 2015

RNA is a polymeric molecule implicated in various biological processes, such as the coding, decoding, regulation, and expression of genes. Numerous studies have examined RNA features using whole transcriptome sequencing (RNA-seq) approaches. RNA-seq is a powerful technique for characterizing and quantifying the transcriptome and accelerates the development of bioinformatics software. In this review, we introduce routine RNA-seq workflow together with related software, focusing particularly on transcriptome reconstruction and expression quantification.

• Journal of Microbiology and Biotechnology
• /
• v.25 no.6
• /
• pp.765-770
• /
• 2015

Recent sequencing technology development has revolutionized fields of microbial ecology. MiSeq-based microbial community analysis allows us to sequence more than a few hundred samples at a time, which is far more cost-effective than pyrosequencing. The approach, however, has not been preferably used owing to computational difficulties of processing huge amounts of data as well as known Illumina-derived artefact problems with amplicon sequencing. The choice of assembly software to take advantage of paired-end sequencing and methods to remove Illumina artefacts sequences are discussed. The protocol we suggest not only removed erroneous reads, but also dramatically reduced computational workload, which allows even a typical desktop computer to process a huge amount of sequence data generated with Illumina sequencers. We also developed a Web interface (http://biotech.jejunu.ac.kr/ ~abl/16s/) that allows users to conduct fastq-merging and mothur batch creation. The study presented here should provide technical advantages and supports in applying MiSeq-based microbial community analysis.

• BMB Reports
• /
• v.45 no.7
• /
• pp.377-389
• /
• 2012

Food fermentations have enhanced human health since the dawn of time and remain a prevalent means of food processing and preservation. Due to their cultural and nutritional importance, many of these foods have been studied in detail using molecular tools, leading to enhancements in quality and safety. Furthermore, recent advances in high-throughput sequencing technology are revolutionizing the study of food microbial ecology, deepening insight into complex fermentation systems. This review provides insight into novel applications of select molecular techniques, particularly next-generation sequencing technology, for analysis of microbial communities in fermented foods. We present a guideline for integrated molecular analysis of food microbial ecology and a starting point for implementing next-generation analysis of food systems.

• Genomics & Informatics
• /
• v.18 no.3
• /
• pp.26.1-26.6
• /
• 2020

Single-cell RNA sequencing (scRNA-seq) has been widely applied to provide insights into the cell-by-cell expression difference in a given bulk sample. Accordingly, numerous analysis methods have been developed. As it involves simultaneous analyses of many cell and genes, efficiency of the methods is crucial. The conventional cell type annotation method is laborious and subjective. Here we propose a semi-automatic method that calculates a normalized score for each cell type based on user-supplied cell type-specific marker gene list. The method was applied to a publicly available scRNA-seq data of mouse cardiac non-myocyte cell pool. Annotating the 35 t-stochastic neighbor embedding clusters into 12 cell types was straightforward, and its accuracy was evaluated by constructing co-expression network for each cell type. Gene Ontology analysis was congruent with the annotated cell type and the corollary regulatory network analysis showed upstream transcription factors that have well supported literature evidences. The source code is available as an R script upon request.

• Genomics & Informatics
• /
• v.21 no.1
• /
• pp.11.1-11.5
• /
• 2023

Breast cancer is the most common cancer worldwide, and advanced breast cancer with metastases is incurable mainly with currently available therapies. Therefore, it is essential to understand molecular characteristics during the progression of breast carcinogenesis. Here, we report a dataset of whole genomes from the human mammary epithelial cell system derived from a reduction mammoplasty specimen. This system comprises pre-stasis 184D cells, considered normal, and seven cell lines along cancer progression series that are immortalized or additionally acquired anchorage-independent growth. Our analysis of the whole-genome sequencing (WGS) data indicates that those seven cancer progression series cells have somatic mutations whose number ranges from 8,393 to 39,564 (with an average of 30,591) compared to 184D cells. These WGS data and our mutation analysis will provide helpful information to identify driver mutations and elucidate molecular mechanisms for breast carcinogenesis.

• Korean Journal of Veterinary Service
• /
• v.42 no.4
• /
• pp.297-300
• /
• 2019

In countries with FMD vaccination, as in Korea, typical clinical signs do not appear, and even in FMD positive cases, it is difficult to isolate the FMDV or obtain whole genome sequence. To overcome this problem, more rapid and simple NGS system is required to control FMD in Korea. FMDV (O/Boeun/ SKR/2017) RNA was extracted and sequenced using Ion Torrent's bench-top sequencer with amplicon panel with optimized bioinformatics pipelines. The whole genome sequencing of raw data generated data of 1,839,864 (mean read length 283 bp) reads comprising a total of 521,641,058 (≥Q20 475,327,721). Compared with FMDV (GenBank accession No. MG983730), the FMDV sequences in this study showed 99.83% nucleotide identity. Further study is needed to identify these differences. In this study, fast and robust methods for benchtop next generation sequencing (NGS) system was developed for analysis of Foot-and-mouth disease virus (FMDV) whole genome sequences.