• Journal of Animal Science and Technology
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• 제65권2호
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• pp.473-477
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• 2023

Lactobacillus amylovorus CACC736 was originated from swine feces in Korea. The complete genome sequences of the strain contained one circular chromosome (2,057,809 base pair [bp]) with 38.2% guanine-cytosine (GC) content and two circular plasmids, namely, pCACC736-1 and pCACC736-2. The predicted protein-coding genes, which are encoding the clustered regularly interspaced short palindromic repeats (CRISPR)-associated proteins, biosynthesis of bacteriocin (helveticin J), and the related proteins of the bile, acid tolerance. Notably, the genes related to vitamin B-group biosynthesis (riboflavin and cobalamin) were also found in L. amylovorus CACC736. Collectively, the complete genome sequence of the L. amylovorus CACC736 will aid in the development of functional probiotics in the animal industry.

• 한국미생물·생명공학회지
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• 제51권3호
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• pp.296-299
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• 2023

We present the complete genome sequence of Priestia aryabhattai strain S2 isolated from the soybean rhizosphere. The genome consists of a single circular chromosome of 5,070,860 bp with a G+C content of 38.3% and 2 plasmids, P1(148,124 bp, GC content 33.3%) and P2 (76,418 bp, GC content 36.5%).

• Molecules and Cells
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• 제37권2호
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• pp.149-160
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• 2014

Plant breeders have focused on improving plant architecture as an effective means to increase crop yield. Here, we identify the main-effect quantitative trait loci (QTLs) for plant shape-related traits in rice (Oryza sativa) and find candidate genes by applying whole genome re-sequencing of two parental cultivars using next-generation sequencing. To identify QTLs influencing plant shape, we analyzed six traits: plant height, tiller number, panicle diameter, panicle length, flag leaf length, and flag leaf width. We performed QTL analysis with 178 $F_7$ recombinant inbred lines (RILs) from a cross of japonica rice line 'SNU-SG1' and indica rice line 'Milyang23'. Using 131 molecular markers, including 28 insertion/deletion markers, we identified 11 main- and 16 minor-effect QTLs for the six traits with a threshold LOD value > 2.8. Our sequence analysis identified fifty-four candidate genes for the main-effect QTLs. By further comparison of coding sequences and meta-expression profiles between japonica and indica rice varieties, we finally chose 15 strong candidate genes for the 11 main-effect QTLs. Our study shows that the whole-genome sequence data substantially enhanced the efficiency of polymorphic marker development for QTL fine-mapping and the identification of possible candidate genes. This yields useful genetic resources for breeding high-yielding rice cultivars with improved plant architecture.

• 한국동물위생학회지
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• 제39권1호
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• pp.41-49
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• 2016

In the present study, fast and robust methods for the next generation sequencing (NGS) were developed for analysis of PRRSV full genome sequences, which is a positive sensed RNA virus with a high degree of genetic variability among isolates. Two strains of PRRSVs (VR2332 and VR2332-R) which have been maintained in our laboratory were used to validate our methods and to compare with the sequence registered in GenBank (GenBank accession no. EF536003). The results suggested that both of strains had 100% coverage with the reference; the VR2332 had the coverage depth from minimum 3 to maximum 23,012, for the VR2332-R from minimum 3 to maximum 41,348, and 22,712 as an average depth. Genomic data produced from the massive sequencing capacities of the NGS have enabled the study of PRRSV at an unprecedented rate and details. Unlike conventional sequence methods which require the knowledge of conserved regions, the NGS allows de novo assembly of the full viral genomes. Therefore, our results suggested that these methods using the NGS massively facilitate the generation of more full genome PRRSV sequences locally as well as nationally in regard of saving time and cost.

• 미생물학회지
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• 제54권4호
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• pp.477-479
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• 2018

김치로부터 분리한 Lactobacillus koreensis 26-25 균주의 유전체서열을 분석하였다. 균주 26-25의 유전체는 G + C 비율이 49.23%이며, 2,720개의 유전자와 2,556개의 단백질 코딩 유전자, 85개의 위유전자 그리고 78개의 RNA 유전자를 포함한 단일 원형 염색체로 구성되었으면 그 크기는 3,006,812 bp였다. 균주 26-25는 인삼사포닌의 당 분해에 관여하는 여러 타입의 글라이코시다제 유전자를 가지고 있었다. 이러한 지놈 분석은 주요 진세노사이드가 우수한 약리학적 활성의 미량 진세노사이드로 전환하는데 관여하는 유전자 특징을 이해하는데 큰 기여가 되었다.

• 한국응용곤충학회지
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• 제61권3호
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• pp.449-460
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• 2022

광식성 난방제 해충인 파밤나방(Spodoptera exigua)의 친환경적 방제원으로써 이용을 위해 국내에서 분리된 파밤나방 핵다각체병바이러스(S. exigua nucleopolyhedrovirus K1: SeNPV-K1)의 형태 및 전체 유전체 서열을 분석하였다. SeNPV-K1의 다각체(polyhedra)는 0.6-1.8 um 크기의 부정형으로, 기 보고된 SeNPV와 외형적 차이는 보이지 않았다. 전체 유전체의 염기서열을 분석한 결과, 기 보고된 SeNPV와 비교할 때 145 bp 더 많은 135,756 bp로 확인되었으며, G+C 함량은 44% 였고 상동반복영역은 6개로 두 바이러스간에 차이는 없었다. ORF 분석결과, SeNPV-K1은 기 보고된 것과 비교할 때 2개 더 적은 137개를 가지며, SeNPV-K1에만 존재하는 ORF는 4개가 확인되었다. 이들 4개의 ORF는 비필수 유전자로 바이러스의 특성에는 큰 영향을 주지 않을 것으로 여겨졌다. 유전체의 vista 분석 결과, SeNPV-K1과 기 보고된 SeNPV의 전체 염기서열 유사도가 매우 높은 것으로 확인되었다. 국내에서 처음으로 분석한 SeNPV-K1의 전체 유전체는 기 보고된 SeNPV와 유사한 것으로 나타났으나 서로 다른 분리주로 국내 고유자원임을 확인하였다.

• 한국패류학회지
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• 제26권4호
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• pp.317-326
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• 2010

The availability of fast and inexpensive sequencing technology has enabled researchers around the world to conduct many genome sequencing and expressed sequence tag (EST) projects of diverse organisms. In recent years, whole genome projects have been undertaken to sequence ten species from the phylum Mollusca. These include Aplysia californica, Lottia gigantea, Crassostrea virginica, Spisula solidissima, Mytilus californianus, Biomphalaria glabrata, Crepidula fornicata, Elysia chlorotica, Lottia scutum and Radix balthica. Additionally, complete mitochondrial genomes of 91 mollusks have been reported. In Korea, EST projects have been conducted in nine mollusk species that include Nesiohelix samarangae, Pisidium (Neopisidium) coreanum, Physa acuta, Incilaria fruhstorferi, Meretrix lusoria, Ruditapes philippinarum, Nordotis gigantea, Crassostrea gigas and Laternula elliptica. Finally, the mitochondrial genome projects from the Pacific Oyster (Crassostrea gigas) and the rock shell (Thais clavigera) have been conducted and reported. However, no systemic mollusk genome project has so far been conducted in Korea. In this report, the current status and research trends in mollusk genome study in Korea will be discussed.

• 한국멀티미디어학회논문지
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• 제7권3호
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• pp.408-417
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• 2004

유전체 분석 과정은 여러 단계를 걸쳐 다양한 소프트웨어 분석 도구가 사용되는 복잡한 작업을 수반한다. 유전체 분석과 관련된 기존의 소프트웨어 도구들은 대부분 리눅스나 유닉스 기반 프로그램 이므로 생물학자가 이들을 설치하고 사용하는데 어려움과 불편함이 많은 실정이다. 또한, 분석의 각 단계별로 생산되는 파일은 수작업을 통한 변환을 거쳐야만 다음 단계의 입력으로 사용될 수 있다. 근래에 웹을 기반으로한 도구들이 개발되고 있으나 한번에 하나의 서열을 처리하는 방식이므로 대량의 실험 데이터를 분석하는 경우에는 반복 작업으로 인한 시간과 노력이 요구되는 단점을 갖고 있다. 본 논문에서는 유전체 분석에 필요한 여러 도구들을 웹 환경에서 하나의 그래픽 사용자 인터페이스로 통합하여 생물학자들이 보다 쉽게 서열과 기능을 분석할 수 있도록 한 WGAT(Web-based Genome Analysis Tool)를 제안한다. WGAT는 리눅스 서버에 유전체 데이터 분석프로그램을 구동하고, 클라이언트 웹 (web)에서 데이터 파일과 분석에 필요한 선택사항들을 입력함으로써 한번에 여러 단계의 분석 작업을 수작업 없이 자동으로 처리할 수 있다. WGAT시스템의 생산성을 분석하기 위하여 기존의 방식과 WGAT를 이용한 방식의 서열분석 처리 시간을 비교한 결과 서열 단편의 개수가 1000개인 경우 기존의 방식보다 20배 이상 분석 능력이 향상됨을 확인할 수 있었다.

• Mycobiology
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• 제50권4호
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• pp.254-257
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• 2022

Wolfiporia cocos is a wood-decay brown rot fungus belonging to the family Polyporaceae. While the fungus grows, the sclerotium body of the strain, dubbed Bokryeong in Korean, is formed around the roots of conifer trees. The dried sclerotium has been widely used as a key component of many medicinal recipes in East Asia. Wolfiporia cocos strain KMCC03342 is the reference strain registered and maintained by the Korea Seed and Variety Service for commercial uses. Here, we present the first draft genome sequence of W. cocos KMCC03342 using a hybrid assembly technique combining both short- and long-read sequences. The genome has a total length of 55.5 Mb comprised of 343 contigs with N50 of 332 kb and 95.8% BUSCO completeness. The GC ratio was 52.2%. We predicted 14,296 protein-coding gene models based on ab initio gene prediction and evidence-based annotation procedure using RNAseq data. The annotated genome was predicted to have 19 terpene biosynthesis gene clusters, which was the same number as the previously sequenced W. cocos strain MD-104 genome but higher than Chinese W. cocos strains. The genome sequence and the predicted gene clusters allow us to study biosynthetic pathways for the active ingredients of W. cocos.

• Journal of Microbiology and Biotechnology
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• 제26권10호
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• pp.1800-1807
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• 2016

To understand how human cytomegalovirus (HCMV) might change and evolve after reactivation, it is very important to understand how the nucleotide sequence of cultured HCMV changes after in vitro passaging in cell culture, and how these changes affect the genome of HCMV and the consequent variation in amino acid sequence. Strain JHC of HCMV was propagated in vitro for more than 40 passages and its biological and genetic changes were monitored. For each passage, real-time PCR was performed in order to determine the genome copy number, and a plaque assay was employed to get virus infection titers. The infectious virus titers gradually increased with passaging in cell culture, whereas the number of virus genome copies remained relatively unchanged. A linear correlation was observed between the passage number and the log₁₀ infectious virus titer per virus genome copy number. To understand the genetic basis underlying the increase in HCMV infectivity with increasing passage, the whole-genome DNA sequence of the high-passage strain was determined and compared with the genome sequence of the low-passage strain. Out of 100 mutations found in the high-passage strain, only two were located in an open reading frame. A G-T substitution in the RL13 gene resulted in a nonsense mutation and caused an early stop. A G-A substitution in the UL122 gene generated an S-F nonsynonymous mutation. The mutations in the RL13 and UL122 genes might be related to the increase in virus infectivity, although the role of the mutations found in noncoding regions could not be excluded.