• 한국자원식물학회지
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• 제30권6호
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• pp.654-661
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• 2017

Dual-color fluorescence in situ hybridization karyotype analysis was created using repetitive sequences including two types of rDNA repeats (45S and 5S rDNAs) and Arabidopsis-type telomere sequence repeats. The somatic metaphase cells of Carthamus tinctorius were observed as diploids (2n=2x=24). A symmetrical or slightly asymmetrical karyotype with seven pairs of metacentric and five pairs of submetacentric chromosomes was observed. The lengths of the somatic metaphase chromosomes ranged from 4.18 to $6.53{\mu}m$, with a total length of $60.71{\mu}m$. One locus of 45S rDNA was located on the pericentromeric regions of three pairs of chromosomes and the other pair was situated on the terminal regions of the short arms of a single pair of chromosomes. One locus of 5S rDNA was detected on the interstitial regions of the short arms of two pairs of chromosomes. Arabidopsis-type telomeric repeats were detected on the terminal regions of all pairs of chromosomes. Co-localization of loci between telomeric repeats and 45S rDNA was observed in a single pair of chromosomes. The results provide additional information for the existing physical mapping project of C. tinctorius and will also serve as a benchmark to a more intricate cytogenetic investigation of C. tinctorius and its related species.

• 원예과학기술지
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• 제30권6호
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• pp.751-756
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• 2012

Fluorescence in situ hybridization (FISH) is a powerful tool for the detection of DNA sequences in the specific region of the chromosomes. As well as for the integrated physical mapping, FISH karyotype analysis has to be preceded. Karyotype of Raphanus sativus 'Wonkyo 10039' was analyzed by a dual-color FISH technique; using various repetitive DNA probes, including 5S rDNA, 45S rDNA, and centromere retrotransposon. The length of the somatic metaphase chromosome ranged from 1.35 to $2.06{\mu}m$ with a total length of $15.29{\mu}m$. The chromosome complements comprised of eight pairs of metacentrics and one pair of submetacentric. Bleached DAPI Band analysis revealed a heterochromatin region, covering 28.6% to 50.4% each chromosomes. 5S and 45S rDNA sequences were located on two and three pairs of chromosomes, respectively. The centromere retrotransposon of Brassica (CRB) is a major component in Brassica related species that has been maintained as a common centromere component. CRB signals were detected on the centromere and pericentromeric region of R. sativus 'Wonkyo 10039' and three basic Brassica species (B. rapa, B. nigra, and B. oleracea). These results will provide a valuable background for physical mapping and elucidation of the evolutionary relationship among the Brassica related species.

• 한국수산과학회지
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• 제33권6호
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• pp.489-495
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• 2000

The 185 ribosomal RNA gene (185 rDNA) of the marine alga Porphyra sp. 723 (Bangiales, Rhodophyta) was amplified using the polymerase chain reaction and its sequence was analysed. The Porphyra species was a summer strain collected on rocks in upper intertidal zone at Ikidae, Pusan on 23rd July 1999. The fronds were $1{\~}5 cm$ long, monostromatic, and orbicular or ovate shaped, They had spinulate processes at margin of the frond, Comparison of this 185 rDNA sequence with the other Forphyra species indicates that Porphyra sp. 723 has the same 185 rDNA sequence derived from Porphyra suborbiculata (NCBI access number; AB 013180) except one base pair substitution in 2327 base pairs.

• 생태와환경
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• 제54권3호
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• pp.199-208
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• 2021

메타바코딩을 이용한 환경 DNA 분석은 검출 감도가 높아 어류의 생물다양성 평가 및 멸종위기종의 검출에 유용한 기술이다. 이번 연구는 메타바코딩을 이용해 우리나라 담수어류를 대상으로 높은 검출 효율을 보일 수 있는 적합한 분석방법을 확인하기 위해 4가지 분석조건별, 즉 필터(cellulose nitrate filter, glass fiber filter), 추출 키트(DNeasy^® Blood & Tissue Kit, DNeasy^® PowerWater Kit), 프라이머 조합(12S rDNA, 16S rDNA) 그리고 PCR 방법(conventional PCR, touchdown PCR)로 나타나는 Operational Taxonomic Units(OTUs) 수와 종 조성을 비교하였다. Glass fiber filter와 DNeasy^® Tissue & Blood Kit를 이용해 추출한 시료는 12S rDNA와 16S rDNA 프라이머 조합에서 담수어류 OTUs가 가장 많이 검출되었다. 모든 분석조건 중 프라이머 조합에서만 조기어강(Class Actinopterygii) 평균 OTUs 수에서 통계적으로 유의한 차이를 보였고(Non-parametric Wilcoxon Signed Ranks Test, p=0.005), 담수어류 평균 OTUs 수는 유의하지 않았다. 종 조성 비교 결과 역시 프라이머 조합에서 유의한 차이를 보였고(PERMANOVA, Pseudo-F=6.9489, p=0.006), 나머지 분석조건에서는 유의한 차이를 보이지 않았다. NMDS 분석 결과 종 조성은 유사도 65% 기준에서 프라이머 조합에 따라 묶였고, 16S rDNA 프라이머 세트는 주로 멸종위기종인 모래주사(Microphysogobio koreensis), 꼬치동자개(Pseudogobio brevicorpus)가 기여하였고, 12S rDNA 프라이머 세트는 주로 일반종인 피라미(Zacco platypus), 꺽지(Coreoperca herzi) 등이 기여한 것으로 나타났다. 본 연구는 국내 하천에서 채취한 시료에 대한 메타바코딩을 이용한 종 다양성 분석의 기초정보를 제공한다.

• 미생물학회지
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• 제40권3호
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• pp.189-198
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• 2004

강화도 장화리 갯벌 퇴적물 내의 두 층(0-1cm, 6-7cm 깊이)에 서식하는 미생물 군집구조 및 다양성을 비교하기 위해 16S rDNA의 서열에 기초한 말단제한절편 다형성(terminal-restriction fragment length polymorphism ; T-RFLP)분석과 클론의 염기서열 분석을 실시하였다. 제한 효소HhaI을 이용한 T-RFLP분석 결과표층(0-1cm)에서는 다양한 크기(($60{\pm}2$) bp-($667{\pm}2$)bp)의 말단제한절편(T-RF)들이 고른 분포로 나타났으며, 저층(6-7 cm)에서는 ($60{\pm}2$)bp와 ($93{\pm}2$) bp의 T-RF가 우세하게 나타나 표층에 비해 미생물 군집구조가 단순한 것으로 조사되었다. 총 172개의 클론의 16S rDNA부분 염기서열 분석 결과 98% 유사도 수준에서 98%의 클론이 GenBank에 등록된 염기서열 중 배양된 어떤 미생물과도 일치하지 않는 것으로 조사되었으며, 이 중 148개의 클론(86%)이 서로 다른 계통형(phylotype)으로 분류되어 다양한 미생물이 서식하고 있음을 알 수 있었다. 대부분의 클론들은 $\alpha$-, $\gamma$, $\delta$-Proteobacteria, Acidobacteria/Holophaga 그리고 green nonsulfur bacteria 그룹 내에 속하였고, 이 중 Proteobacteria 그룹이 표층에서는 전체의 69%, 저층에서는 46%의 높은 비율을 차지하였다. 또한 황원소의 산화와 환원에 관련된 $\gamma$-Proteobacteria와 $\delta$-Proteobacteria 그룹이 각각 21.5%와 15.7%로 우세하게 나타나 갯벌의 미생물 군집 구조가 혐기성 환경에서의 황환원에 의해 생성된 황의 거동과 밀접한 연관이 있음을 시사하였다.

• The Plant Pathology Journal
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• 제24권3호
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• pp.279-282
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• 2008

This study describes a phytoplasmal disease occurring in Petunia leaves grown in the glasshouse of the National Horticultural Research Institute, Suwon, Korea. Abnormal growth like flattened stem with flower malformation or phyllody was observed from the plant. The DNA extracted from the diseased leaves was amplified using a universal primer pair of P1/P6 derived from the conserved 16S rRNA gene of Mollicutes giving the expected polymerase chain reaction(PCR) product of 1.5 kb. In the nested PCR assays, the expected DNA fragment of 1.1 kb was amplified with the specific primer pair R16F1/R16R1 that was designed on the basis of aster yellows(AY) phytoplasma 16S rDNA sequences. The 1.1 kb PCR products were cloned and nucleotide sequences were determined, and the sequences of the cloned 168 rRNA gene were deposited in the GenBank database under the accession no. of EU267779. Analysis of the homology percent of the 168 rDNA of PFS-K showed the closest relationship with Hydrangea phyllody phytoplasma(AY265215), Brassica napus phytoplasma(EU123466) and AY phytoplasma CHRY(AY180956). Phytoplasma isolated from the diseased Petunia was designated as Petunia flat stem phytoplasma Korean isolate(PFS-K) in this study. Flattened stem occurring in Petunia was confirmed as infection of AY group of phytoplasma by determination of 16S rRNA gene sequences of phytoplasma and microscopic observation of phytoplasma bodies. This is the first report on the phytoplasmal disease in Petunia in Korea.

• 생명과학회지
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• 제26권11호
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• pp.1341-1344
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• 2016

보길도에서 자라고 있는 황칠나무(Dendropanax morbifera)를 구입하여, 캘러스로 유도한 후, ribosomal DNA(nrDNA)의 internal transcribed spacer (ITS) region의 염기서열을 결정하였다 보길도의 황칠나무(Dendropanax morbifera)의 ITS region의 염기서열을 분석한 결과, 총 689염기를 결정하였다. 결정된 689염기 중에서 ITS1은 222 개염기, 5.8S rDNA는 160염기, ITS2는 233염기인 것으로 판명되었다. GenBank의 BLAST 프로그램(http://www.ncbi.nlm.nih.BLAST)을 사용하여 GenBank/EMBL/DDBJ에 등록되어 있는 Dendropanax 속 33의 염기서열을 수집한 후 multiple alignment를 수행한 결과, 유사도는 99.7%(D. chevalieri)에서 92.6%(Dendropanax arboreus)로 나타났으며, 일본황칠나무(D. trifidus)와는 유사도가 99.4%로 판명되었다.

• Journal of Microbiology
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• 제43권1호
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• pp.1-10
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• 2005

We isolated and cultured bacteria inhabiting solar saltern ponds in Taean-Gun, Chungnam Province, Korea. All of the isolated 64 strains were found to be moderately halophilic bacteria, growing in a salt range of 2-20 %, with an optimal concentration of 5% salt. Bacterial diversity among the isolated halophiles was evaluated via RFLP analyses of PCR-amplified 16S rDNAs, followed by phylogenetic analysis of the partial 16S rDNA sequences. The combination of restriction enzyme digestions with HaeIII, CfoI, MspI and RsaI generated 54 distinct patterns. A neighbor-joining tree of the partial 16S rDNA sequences resulted in the division of the 64 strains into 2 major groups, 45 strains of ${\gamma}-Proteobacteria$ (70.3%) and 19 strains of Firmicutes (29.7%). The ${\alpha}-Proteobacteria$ and Cytophaga-Flavobacterium-Bacterioides groups, which were repeatedly found to exist in thalassohaline environments, were not represented in our isolates. The ${\gamma}-Proteobacteria$ group consisted of several subgroups of the Vibrionaceae (37.5%), Pseudoalteromonadaceae (10.9%), Halomonadaceae (7.8%), Alteromonadaceae (7.8%), and Idiomarinaceae (6.3%). Members of Salinivibrio costicola (29.7%) were the most predominant species among all of the isolates, followed by Halobacillus treperi (12.5%). Additionally, three new species candidates were found, based on similarities of the 16S rDNA sequences to those of previously published species.

• Journal of Microbiology
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• 제41권4호
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• pp.312-319
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• 2003

In an attempt to develop a method for rapid and accurate identification of six Vibrio species that are clinically important and most frequently detected in Korea, 16S rDNA restriction fragment length polymorphism (RFLP) of Vibrio type strains, as well as environmental isolates obtained from the Korean coastal area, was analyzed using ten restriction endonucleases. Digestion of the 16S rDNA fragments amplified by polymerase chain reaction (PCR) with the enzymes gave rise to 2~6 restriction patterns for each digestion for 47 Vibrio strains and isolates. An additional 2~3 restriction patterns were observed for five reference species, including Escherichia coli, Aeromonas hydrophila, A. salmonicida, Photobacterium phosphoreum, and Plesiomonas shigelloides. A genetic distance tree based on RFLP of the bacterial species correlated well with that based on 16S rDNA sequences. The very small 16S rDNA sequence difference (0.1%) between V. alginolyticus and V. parahaemolyticus was resolved clearly by RFLP with a genetic distance of more than 2%. RFLP variation within a species was also detected in the cases of V. parahaemolyticus, V. proteolyticus, and V. vulnificus. According to the RFLP analysis, six Vibrio and five reference species were assigned to 12 genotypes. Using three restriction endonucleases to analyze RFLP proved sufficient to identify the six pathogenic Vibrio species.

• 생명과학회지
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• 제13권6호
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• pp.856-864
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• 2003

원핵생물 (Procaryote)의 분류에 16S rRNA유전자가 많이 이용되어 있으나 제한된 해상력과 유전자의 수에 차이가 있는 등의 문제가 있어 이를 보완할 수 있는 새로운 생체분자를 찾고 그 분류 결과를 16S rRNA의 결과와 비교하였다. COG (Clusters of Orthologous of protein) 방법을 이용하여 43종의 미생물중에서 진핵생물을 제외한 42종의 원핵생물 (procaryote)에서만 발견되는 3종류의 COG인 Transcription elongation factor인 COG0195과 bacterial DNA primase인 COG0358 그리고 uridylate kinase인 COG0528를 구하였다. 이중 유사도와 유전자 수를 바탕으로 새로운 분류의 키로 uridylate kinase를 설정하여 분석한 결과, 같은 속 (genus)에 속하는 세균들은 아주 높은bootstrap value를 갖고 분류도에서 같은 위치에 분포하고 고세균 (Archaebacteria) 내부의 응집성이 높은 등의 유사성을 보였다. 한편 alpha와 epsilon 그룹의 Proteobacteria가 분류도에서 다르게 위치하고 진정세균 (Eubacteria)의 Spi-rochaetales에 속하는 Treponema pallidum (Tpa)와 Borrelia burgdorferi (Bbu)가 고세균과 유연관계가 높게 나타나는 등 차이점도 보였다. Uridylate kinase를 이용한 분류는, 아주 높은 보존성에 의해서 생기는 16S rRNA 유전자를 이용한 문제점을 보완하여 원핵생물의 정확한 분류에 기여할 수 있을 것으로 사료되었다.