• Genomics & Informatics
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• 제15권4호
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• pp.128-135
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• 2017

As next-generation sequencing technologies have advanced, enormous amounts of whole-genome sequence information in various species have been released. However, it is still difficult to assemble the whole genome precisely, due to inherent limitations of short-read sequencing technologies. In particular, the complexities of plants are incomparable to those of microorganisms or animals because of whole-genome duplications, repeat insertions, and Numt insertions, etc. In this study, we describe a new method for detecting misassembly sequence regions of Brassica rapa with genotyping-by-sequencing, followed by MadMapper clustering. The misassembly candidate regions were cross-checked with BAC clone paired-ends library sequences that have been mapped to the reference genome. The results were further verified with gene synteny relations between Brassica rapa and Arabidopsis thaliana. We conclude that this method will help detect misassembly regions and be applicable to incompletely assembled reference genomes from a variety of species.

• Parasites, Hosts and Diseases
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• 제53권5호
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• pp.641-645
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• 2015

Fascioliasis, a food-borne trematode zoonosis, is a disease primarily in cattle and sheep and occasionally in humans. Water dropwort (Oenanthe javanica), an aquatic perennial herb, is a common second intermediate host of Fasciola, and the fresh stems and leaves are widely used as a seasoning in the Korean diet. However, no information regarding Fasciola species contamination in water dropwort is available. Here, we collected 500 samples of water dropwort in 3 areas in Korea during February and March 2015, and the water dropwort contamination of Fasciola species was monitored by DNA sequencing analysis of the Fasciola hepatica and Fasciola gigantica specific mitochondrial cytochrome c oxidase subunit 1 (cox1) and nuclear ribosomal internal transcribed spacer 2 (ITS-2). Among the 500 samples assessed, the presence of F. hepatica cox1 and 1TS-2 markers were detected in 2 samples, and F. hepatica contamination was confirmed by sequencing analysis. The nucleotide sequences of cox1 PCR products from the 2 F. hepatica-contaminated samples were 96.5% identical to the F. hepatica cox1 sequences in GenBank, whereas F. gigantica cox1 sequences were 46.8% similar with the sequence detected from the cox1 positive samples. However, F. gigantica cox1 and ITS-2 markers were not detected by PCR in the 500 samples of water dropwort. Collectively, in this survey of the water dropwort contamination with Fasciola species, very low prevalence of F. hepatica contamination was detected in the samples.

• 대한본초학회지
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• 제28권6호
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• pp.9-14
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• 2013

Objectives : Cnidii Fructus is prescribed as the fruit of Cnidium monnieri (L.) Cusson or Torilis japonica (Houtt.) DC. in Korea pharmacopoeia. Although there are differences in the composition of useful components, two species have been used without distinction. In order to discriminate them, DNA sequencing and taste pattern analysis were used in this study. Methods : Primers ITS 1 and ITS 4 were used to amplify the intergenic transcribed spacer(ITS) region of nuclear ribosomal DNA from seven T. japonica and six C. monnieri samples. Taste pattern of samples were measured by using taste-sensing system SA402B equipped with five foodstuff sensors(CT0, C00, AAE, CA0, and AE1). The five initial taste(sourness, bitterness, astringency, umami, and saltiness) and three aftertaste(aftertaste of bitterness, astringency, and umami) of two species were compared. Results : According to the results of ITS region sequence analysis, two species showed 94 base pairs differences. The similarity of two sequences was 85%. From the taste pattern analysis, sourness, bitterness, aftertaste of bitterness(aftertaste-B), and umami showed a different pattern. Especially, bitterness and aftertaste-B of C. monnieri were significantly higher than T. japonica. In addition, two species were shown to have two markedly different clustering by these two flavors. Conclusion : T. japonica and C. monnieri were effectively discriminated using DNA sequencing and taste pattern analysis. These methods can be used to identify the origin of traditional medicine in order to maintain therapeutic efficacy.

• Journal of Veterinary Science
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• 제22권6호
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• pp.66.1-66.9
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• 2021

Background: Maedi/Visna virus (MVV) is a contagious viral pathogen that causes considerable economic losses to the sheep industry worldwide. Objectives: In China, MVV has been detected in several regions, but its molecular characteristics and genetic variations were not thoroughly investigated. Methods: Therefore, in this study, we conducted next-generation sequencing on an MVV strain obtained from northwest China to reveal its genetic evolution via phylogenetic analysis. Results: A MVV strain obtained from Inner Mongolia (NM) of China was identified. Sequence analysis indicated that its whole-genome length is 9193 bp. Homology comparison of nucleotides between the NM strain and reference strains showed that the sequence homology of gag and env were 77.1%-86.8% and 67.7%-75.5%, respectively. Phylogenetic analysis revealed that the NM strain was closely related to the reference strains isolated from America, which belong to the A2 type. Notably, there were 5 amino acid insertions in variable region 4 and a highly variable motif at the C-terminal of the surface glycoprotein (SU5). Conclusions: The present study is the first to show the whole-genome sequence of an MVV obtained from China. The detailed analyses provide essential information for understanding the genetic characteristics of MVV, and the results enrich the MVV library.

• BMB Reports
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• 제49권12호
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• pp.653-654
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• 2016

The human reference genome, maintained by the Genome Reference Consortium, is conceivably the most complete genome assembly ever, since its first construction. It has continually been improved by incorporating corrections made to the previous assemblies, thanks to various technological advances. Many currently-ongoing population sequencing projects have been based on this reference genome, heightening hopes of the development of useful medical applications of genomic information, thanks to the recent maturation of high-throughput sequencing technologies. However, just one reference genome does not fit all the populations across the globe, because of the large diversity in genomic structures and technical limitations inherent to short read sequencing methods. The recent success in de novo construction of the highly contiguous Asian diploid genome AK1, by combining single molecule technologies with routine sequencing data without resorting to traditional clone-by-clone sequencing and physical mapping, reveals the nature of genomic structure variation by detecting thousands of novel structural variations and by finally filling in some of the prior gaps which had persistently remained in the current human reference genome. Now it is expected that the AK1 genome, soon to be paired with more upcoming de novo assembled genomes, will provide a chance to explore what it is really like to use ancestry-specific reference genomes instead of hg19/hg38 for population genomics. This is a major step towards the furthering of genetically-based precision medicine.

• Genomics & Informatics
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• 제15권4호
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• pp.136-141
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• 2017

Accurate detection of genomic alterations, especially druggable hotspot mutations in tumors, has become an essential part of precision medicine. With targeted sequencing, we can obtain deeper coverage of reads and handle data more easily with a relatively lower cost and less time than whole-exome or whole-genome sequencing. Recently, we designed a customized gene panel for targeted sequencing of major solid cancers. In this study, we aimed to validate its performance. The cancer panel targets 95 cancer-related genes. In terms of the limit of detection, more than 86% of target mutations with a mutant allele frequency (MAF) <1% can be identified, and any mutation with >3% MAF can be detected. When we applied this system for the analysis of Acrometrix Oncology Hotspot Control DNA, which contains more than 500 COSMIC mutations across 53 genes, 99% of the expected mutations were robustly detected. We also confirmed the high reproducibility of the detection of mutations in multiple independent analyses. When we explored copy number alterations (CNAs), the expected CNAs were successfully detected, and this result was confirmed by target-specific genomic quantitative polymerase chain reaction. Taken together, these results support the reliability and accuracy of our cancer panel in detecting mutations. This panel could be useful for key mutation profiling research in solid tumors and clinical translation.

• 디지털융복합연구
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• 제10권6호
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• pp.189-196
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• 2012

본 논문에서는 학습자들의 다자간 협력학습을 위한 스콤 기반 시퀀싱 & 네비게이션 모델을 제안한다. 이 모델은 정형적 접근 방법을 기반으로 하고 있으며, 협력학습을 효율적이고 그래픽적으로 정의하기 위하여 스콤에서의 콘텐츠 집합 모델과 시퀀싱 및 네비게이션 모델에 관하여 ICN(Information Control Net) 모델을 기반으로 정의한다. ICN 모델은 프로세스를 기반으로 각 요소들의 제어 흐름을 표현하는 모델인데, 본 논문에서는 이러한 ICN 모델을 확장한 SCOSNCN(SCO Sequencing & Navigation Control Net) 모델을 활용하여 프로세스의 실행 순서 및 학습 활동을 정의하고 협력학습에 필요한 콘텐츠와 그에 따른 시퀀싱 & 네비게이션 모델 관련 사항들을 정의한다. SCOSNCN 모델에서는 협력학습을 지원하기 위해 각각의 액티비티에 교수자 및 학습자를 정의하고, 정의되어진 액티비티의 선행, 후행 조건 및 네비게이션 조건 등을 명시하여 협력학습을 위한 시퀀싱 & 네비게이션 모델을 제시한다. 또한, 협력학습 정의에 필요한 시퀀싱 & 네비게이션 기본 요소 및 역할, 그리고 이에 대한 규칙 등을 제안한다. 이에 스콤 기반 협력학습을 위한 시퀀싱 & 네비게이션 모델을 바탕으로 스콤 기반 협력학습시스템 아키텍처와 실례를 제안함으로서 향후 교수자 및 학습자뿐만 아니라 e-러닝 산업 분야 및 교육에 있어 학습 콘텐츠의 정의 및 협력학습을 통한 교육의 효율성 향상에 기여하고자 한다.

• 대한의생명과학회지
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• 제9권3호
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• pp.167-170
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• 2003

Cytochrome $b_{5}$($b_{5}$) can be found in a variety of tissues and plays a role in the electron transfer pathways. Several retropseudogenes (numbered as I, II, II, IV, V) have been identified and well investigated for their structures. However, retropseudogene I is not clear in terms of its location on the chromosome. In addition the structure and the exression of retropseudogene V have not been confirmed. To examine the structure of bs retropseudogenes V and to see whether it is expressed in human blood we applied recombinant DNA technologies including polymerase chain reaction (PCR) and DNA sequencing. Retropseudogene V turned out to contain open reading frame (ORF) within its structure, however, no evidence of its expression was detected. Retropseudogene I was also found on the chromosome V. This study should contribute to the understanding of the structure of bs gene family.

• 한국버섯학회지
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• 제4권2호
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• pp.43-47
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• 2006

국내에서 재배하여 생산되고 있는 상황버섯의 일종인 PMO-P4균주에 대한 ITS 영역의 염기서열 분석을 실시하였으며 목질 진흙버섯으로 잘 알려져 있는 P. linteus와 함께 RFLP분석을 통하여 상호 비교한 결과 PMO-P4균주는 P. baumii로 판명되었다. 이 결과를 토대로 이미 보고되어 있는 Phellinus속 균주들과의 종간 ITS 영역의 상동성을 비교한 결과 48.6%-72.2%였으며 본 연구에서 비교한 종들 가운데서는 P. linteus와 상동성이 가장 높았으며 P. gilvus와 상동성이 가장 낮았다.

• Genomics & Informatics
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• 제6권2호
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• pp.87-90
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• 2008

During the last four years, the pyrosequencing-based 454 platform has rapidly displaced the traditional Sanger sequencing method due to its high throughput and cost effectiveness. Meanwhile, the Sanger sequencing methodology still provides the longest reads, and paired-end sequencing that is based on that chemistry offers an opportunity to ensure accurate assembly results. In this report, we describe an optimized approach for hybrid de novo genome assembly using pyrosequencing data and varying amounts of Sanger-type reads. 454 platform-derived contigs can be used as single non-breakable virtual reads or converted to simpler contigs that consist of editable, overlapping pseudoreads. These modified contigs maintain their integrity at the first jumpstarting assembly stage and are edited by fragmenting and rejoining. Pre-existing assembly software then can be applied for mixed assembly with 454-derived data and Sanger reads. An effective method for identifying genomic differences between reference and sample sequences in whole-genome resequencing procedures also is suggested.