Draft Genome Sequence of a Chitinase-producing Biocontrol Bacterium Serratia sp. C-1

Park, Seur Kee,Kim, Young Cheol The Korean Society of Plant Pathology 2015 식물병연구 Vol.21 No.3

The chitinase-producing bacterial strain C-1 is one of the key chitinase-producing biocontrol agents used for effective bioformulations for biological control. These bioformulations are mixed cultures of various chitinolytic bacteria. However, the precise identification, biocontrol activity, and the underlying mechanisms of the strain C-1 have not been investigated so far. Therefore, we evaluated in planta biocontrol efficacies of C-1 and determined the draft genome sequence of the strain in this study. The bacterial C-1 strain was identified as a novel Serratia sp. by a phylogenic analysis of its 16S rRNA sequence. The Serratia sp. C-1 bacterial cultures showed strong in planta biocontrol efficacies against some major phytopathogenic fungal diseases. The draft genome sequence of Serratia sp. C-1 indicated that the C-1 strain is a novel strain harboring a subset of genes that may be involved in its biocontrol activities.

Draft Genome Sequence of a Chitinase-producing Biocontrol Bacterium Serratia sp. C-1

박서기,김영철 한국식물병리학회 2015 식물병연구 Vol.21 No.3

The chitinase-producing bacterial strain C-1 is one of the key chitinase-producing biocontrol agents used for effective bioformulations for biological control. These bioformulations are mixed cultures of various chitinolytic bacteria. However, the precise identification, biocontrol activity, and the underlying mechanisms of the strain C-1 have not been investigated so far. Therefore, we evaluated in planta biocontrol efficacies of C-1 and determined the draft genome sequence of the strain in this study. The bacterial C-1 strain was identified as a novel Serratia sp. by a phylogenic analysis of its 16S rRNA sequence. The Serratia sp. C-1 bacterial cultures showed strong in planta biocontrol efficacies against some major phytopathogenic fungal diseases. The draft genome sequence of Serratia sp. C-1 indicated that the C-1 strain is a novel strain harboring a subset of genes that may be involved in its biocontrol activities.

Draft genome sequence of a Flavobacterium chungbukense CS100T isolated from soil

오지성,노동현 한국미생물학회 2022 미생물학회지 Vol.58 No.4

The draft genome sequence of Flavobacterium chungbukense CS100T isolated from soil was determined using Illumuna Hiseq X-ten platform. The assembled genome consists of 18 scaffolds with a total length of 5,355,850 bp with N50 values of 851,609 bp. The genomic DNA G + C content was 33.5%. The draft genome encoded 4,436 protein-coding genes, 8 rRNA genes, 52 tRNA genes, 3 non-coding RNA genes and 53 pseudogenes. The genome sequence of this type strain in the genus Flavobacterium will be used for reference to taxonomical classification based on the genome. Additionally, several useful genes in the genome related to antimicrobials, moisturizer and pigments production, and the degradation of aromatic compounds and biopolymers might be used for industrial applications.

Draft genome sequence of lytic bacteriophage CP3 infecting anaerobic bacterial pathogen Clostridium perfringens

김영주,고세영,연영은,한범구,김현일,오창식,김동혁,Kim, Youngju,Ko, Seyoung,Yeon, Young Eun,Le, Hoa Thi,Han, Beom Ku,Kim, Hyunil,Oh, Chang-Sik,Kim, Donghyuk The Microbiological Society of Korea 2018 미생물학회지 Vol.54 No.2

Clostridium perfringens는 그람 양성, 막대 모양, 혐기성, 포자 형성을 하는 병원균으로서 Clostridiaceae과에 속한다. C. perfringens는 인간의 장관과 척추동물 내에서 식중독을 포함하는 질병을 유발한다. 높은 특이성으로 목표 세균을 죽이는 박테리오파지는 병원세균을 제어하는 방법들 중 하나로 여겨져 왔다. 본 연구에서는 C. perfringens를 감염시킬 수 있는 박테리오 파지 CP3의 유전체 염기서열 초안을 보고한다. 본 박테리오파지의 G + C 비율은 34.0%이며, 52,068 bp로 구성된 유전체 DNA를 지니고 있었다. 이 유전체는 74개의 단백질 유전자를 포함하고 있었으며, RNA는 확인되지 않았다. Clostridium perfringens is a Gram-positive, rod-shaped, anaerobic, spore-forming pathogenic bacterium, which belongs to the Clostridiaceae family. C. perfringens causes diseases including food poisoning in vertebrates and intestinal tract of humans. Bacteriophages that can kill target bacteria specifically have been considered as one of control methods for bacterial pathogens. Here, we report a draft genome sequence of the bacteriophage CP3 effective to C. perfringens. The phage genome comprises 52,068 bp with a G + C content of 34.0%. The draft genome has 74 protein-coding genes, 29 of which have predicted functions from BLASTp analysis. Others are conserved proteins with unknown functions. No RNAs were found in the genome.

Draft genome sequence of Peribacillus sp. AGMB 02131 isolated from feces of a Korean cow

지앙링민,정원용,박승환,강세원,이미경,이정숙,이주혁,이지영 한국미생물학회 2021 미생물학회지 Vol.57 No.1

Peribacillus sp. AGMB 02131 was isolated from the feces of a Korean cow. Here, we report the draft genome sequence of the strain AGMB 02131 based on Nova SeqTM 6000 sequencing system (Illumina). The genome comprises 70 contigs with a chromosome length of 4,038,965 bp and 38.5% GC content. The draft genome contains 3,806 protein-coding genes, 51 pseudogenes, 112 RNA genes including 17 ribosomal RNA genes (7 5S rRNA, 7 16S rRNA, 3 23S rRNA), 90 transfer RNA (tRNA) genes, and 5 non-coding RNA (ncRNA) genes. Additionally, genes involved in the fatty acid metabolism (biosynthesis, elongation, and degradation) and bile acid biosynthesis (primary and secondary) were identified throughout the draft genome, which might be crucial for promoting gut epithelial lining to regulate the animal’s health and digestion. Moreover, insulin, antimicrobial, and antineoplastic drug resistance-related genes were also presented in this genome.

Draft genome sequence of an Alteromonadaceae bacterium BrNp21-10 isolated from seawater

오지성,노동현 한국미생물학회 2023 미생물학회지 Vol.59 No.4

The draft genome sequence of an Alteromonadaceae bacterium BrNp21-10 isolated from coastal seawater was determined using the Illumina Hiseq X-ten platform. The assembled genome consists of 33 contigs totaling 4,217,876 bp with N50 values of 212,777 bp. The genomic DNA G + C content was 42.5%. The draft genome comprised 3,674 protein-coding, 5 rRNA, 48 tRNA, 4 non-coding RNA genes, and 15 pseudogenes. There were a series of genes related to CRISPR, flagellar assembly, and assimilatory sulfate reduction in the genome. The isolated strain BrNp21-10 is considered to be a novel strain belonging to the family Alteromonadaceae by 16S rRNA gene sequence and digital DDH analysis.

개 회충 게놈 응용 사례에서 공개용 분석 툴을 사용한 드래프트 게놈 어셈블리 생성

원정임(JungIm Won),공진화(JinHwa Kong),허선(Sun Huh),윤지희(JeeHee Yoon) 한국정보과학회 2014 정보과학회 컴퓨팅의 실제 논문지 Vol.20 No.9

NGS 기술의 발달로 시퀀싱 비용이 급격히 하락됨에 따라 대규모 크기의 유전체 염기 서열 해독을 소규모의 실험실에서 수행할 수 있게 되었다. 디노버 어셈블리는 표준 유전체가 없는 새로운 종을 시퀀싱하는 경우 리드들의 염기 서열 정보를 이용하여 재구성함으로써 원래의 전체 시퀀스를 복원하는 것이다. 최근 이와 관련된 많은 연구 결과가 보고되고 있으나, 충분한 분석 노하우와 명확한 가이드라인 등이 공개되어 있지 않기 때문에 이들 연구에서 제시하는 동일한 어셈블리 수행 과정 및 분석 툴들을 사용하더라도 만족할만한 수준의 어셈블리 결과를 얻지 못하는 경우가 발생한다. 본 연구에서는 이러한 문제점을 해결하기 위하여 NGS 기술과 디노버 어셈블리 기술을 이용하여 아직 밝혀지지 않은 생물체의 전체 DNA의 염기 서열을 밝히기 위한 일련의 과정들을 단계별로 소개하고, 각 단계에서 필요로 하는 공개용 분석 툴의 장단점을 분석하여 제시한다. 이러한 과정별 단계를 구체적으로 설명하기 위하여 본 연구에서는 350Mbp 크기의 개 회충 게놈을 응용 사례로 사용한다. 또한 디노버 어셈블리 과정을 통해 새롭게 어셈블리된 시퀀스와 다른 유사 종과의 상동성 분석을 수행하여 어셈블리된 시퀀스에서의 유전자 영역 추출과 추출된 유전자의 기능을 예측한다. It has become possible for small scale laboratories to interpret large scale genomic DNA, thanks to the reduction of the sequencing cost by the development of next generation sequencing (NGS). De novo assembly is a method which creates a putative original sequence by reconstructing reads without using a reference sequence. There have been various study results on de novo assembly, however, it is still difficult to get the desired results even by using the same assembly procedures and the analysis tools which were suggested in the studies reported. This is mainly because there are no specific guidelines for the assembly procedures or know-hows for the use of such analysis tools. In this study, to resolve these problems, we introduce steps to finding whole genome of an unknown DNA via NGS technology and de novo assembly, while providing the pros and cons of the various analysis tools used in each step. We used 350Mbp of Toxocara canis DNA as an application case for the detailed explanations of each stated step. We also extend our works for prediction of protein-coding genes and their functions from the draft genome sequence by comparing its homology with reference sequences of other nematodes.

Development of a Species-specific PCR Assay for Three Xanthomonas Species, Causing Bulb and Flower Diseases, Based on Their Genome Sequences

Back, Chang-Gi,Lee, Seung-Yeol,Lee, Boo-Ja,Yea, Mi-Chi,Kim, Sang-Mok,Kang, In-Kyu,Cha, Jae-Soon,Jung, Hee-Young The Korean Society of Plant Pathology 2015 Plant Pathology Journal Vol.31 No.3

In this study, we developed a species-specific PCR assay for rapid and accurate detection of three Xanthomonas species, X. axonopodis pv. poinsettiicola (XAP), X. hyacinthi (XH) and X. campestris pv. zantedeschiae (XCZ), based on their draft genome sequences. XAP, XH and XCZ genomes consist of single chromosomes that contain 5,221, 4,395 and 7,986 protein coding genes, respectively. Species-specific primers were designed from variable regions of the draft genome sequence data and assessed by a PCR-based detection method. These primers were also tested for specificity against 17 allied Xanthomonas species as well as against the host DNA and the microbial community of the host surface. Three primer sets were found to be very specific and no amplification product was obtained with the host DNA and the microbial community of the host surface. In addition, a detection limit of $1pg/{\mu}l$ per PCR reaction was detected when these primer sets were used to amplify corresponding bacterial DNAs. Therefore, these primer sets and the developed species-specific PCR assay represent a valuable, sensitive, and rapid diagnostic tool that can be used to detect three specific pathogens at early stages of infection and may help control diseases.

Development of a Species-specific PCR Assay for Three Xanthomonas Species, Causing Bulb and Flower Diseases, Based on Their Genome Sequences

백창기,이승열,이부자,예미지,김상목,강인규,차재순,정희영 한국식물병리학회 2015 Plant Pathology Journal Vol.31 No.3

In this study, we developed a species-specific PCR assay for rapid and accurate detection of three Xanthomonas species, X. axonopodis pv. poinsettiicola (XAP), X. hyacinthi (XH) and X. campestris pv. zantedeschiae (XCZ), based on their draft genome sequences. XAP, XH and XCZ genomes consist of single chromosomes that contain 5,221, 4,395 and 7,986 protein coding genes, respectively. Species-specific primers were designed from variable regions of the draft genome sequence data and assessed by a PCR-based detection method. These primers were also tested for specificity against 17 allied Xanthomonas species as well as against the host DNA and the microbial community of the host surface. Three primer sets were found to be very specific and no amplification product was obtained with the host DNA and the microbial community of the host surface. In addition, a detection limit of 1 pg/μl per PCR reaction was detected when these primer sets were used to amplify corresponding bacterial DNAs. Therefore, these primer sets and the developed species-specific PCR assay represent a valuable, sensitive, and rapid diagnostic tool that can be used to detect three specific pathogens at early stages of infection and may help control diseases.

살조성 세균 Halobacillus sp. Nhm2S1의 유전체 염기서열 분석

오지성,노동현 한국미생물학회 2021 미생물학회지 Vol.57 No.3

An algicidal bacterium, designated strain Nhm2S1, was isolated from tidal flat of South Sea, Korea. Herein, we report draft genome sequence of strain Nhm2S1, which was determined using Illumina HiSeq X-ten platform. The assembled genome of strain Nhm2S1 consists of 10 contigs with a total length of 3,926,919 bp and the genomic DNA G + C content was 43.4 mol%. The draft genome encoded 3,876 protein-coding genes, 11 rRNA genes, 65 tRNA genes, 4 non-coding RNA genes and 26 pseudo genes. The genome contained genes (redP/R) involved in the biosynthesis of the algicidal pigment prodigiosin, which was thought to helpful in understanding of algae-killing properties. 살조성 세균 Nhm2S1 균주는 남해의 갯벌로부터 분리되었 다. 본 연구에서는 Illumuna Hiseq X-ten platform을 사용하여 Nhm2S1 균주의 유전체 서열을 수행하였다. Nhm2S1 균주의 조립된 유전체는 10개의 contig로 구성되었고, 염색체 길이는 3,926,919 bp이며 43.4 mol% G + C 함량을 지니고 있었다. 유 전체는 3,876개의 단백질 암호 유전자, 11개의 rRNA 유전자, 65개의 tRNA 유전자, 4개의 non-coding RNA 유전자 및 26 위 유전자(pseudo gene)를 암호화하였다. 게놈에는 살조성 색소 프로디지오신의 생합성에 관여하는 유전자(redP/R)가 포함 되어 있어 살조 특성을 이해하는 데 도움이 될 것이다.