• Title/Summary/Keyword: I8S rDNA

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DNA Barcoding of Benthic Ragworms of the Genus Nectoneanthes (Polychaeta: Nereididae) Collected in Korean Waters

  • Park, Taeseo
    • Animal Systematics, Evolution and Diversity
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    • v.37 no.3
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    • pp.235-241
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    • 2021
  • To provide better taxonomic information of the genus Nectoneanthes, the two DNA barcode regions of mitochondrial cytochrome c oxidase subunit I (COI) and 16S ribosomal DNA (rDNA) sequences of Nectoneanthes oxypoda and N. uchiwa were determined. In addition, the respective sequences of four nereidid species closely related to Nectoneanthes were retrieved from GenBank for comparison and to estimate intra- and inter-specific genetic distances. The aligned sequence lengths of COI and 16S rDNA were 570 bp and 419 bp long, respectively. The mean intraspecific variation in both markers was less than 1% in all species except for that in COI of H. diadroma (1.87%). The mean interspecific variation between N. oxypoda and N. uchiwa was 12.02% regarding COI and 1.85% regarding 16S rDNA. In contrast, the mean interspecific variation between species of other genera was comparably higher(i.e., genus Perinereis: 20.5% in COI and 8.3% in 16S rDNA; genus Hediste: 13.18% in COI and 2.64% in 16S rDNA), compared with that between the two Nectoneanthes species. This result indicated that these Nectoneanthes species are genetically more closely related than other congeneric species of different genera. The DNA barcoding information on Nectoneanthes species generated in this study provides valuable insights for further biodiversity studies on nereidid species.

The Diversity of Culturable Organotrophic Bacteria from Local Solar Salterns

  • Yeon, Sun-Hee;Jeong, Won-Jin;Park, Jin-Sook
    • Journal of Microbiology
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    • v.43 no.1
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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.

Comparison of Relationships in Infraspecies of Magnaporthe grisea Using DNA Sequence of Internal Transcribed Spacer II Region in Ribosomal DNA (도열병균(Magnaporthe grisea)의 Ribosomal DNA의 ITS II 부위 핵산 염기서열을 이용한 균주간 근연관계 비교)

  • 배신철;이신우;이인구;예완해;류진창
    • Korean Journal Plant Pathology
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    • v.12 no.1
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    • pp.91-98
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    • 1996
  • 벼도열병균 14개 균주와 벼 이외 화본과 식물 도열병균 12개 균주를 대상으로 rDNA의 ITS II 부위를 증폭하여 그들의 핵산 구조 차이를 분석함으로 도열병균 균주간 분류를 시도하였다. 5.8S rDNA의 3`-말단 부위와 28S rDNA의 5`-말단 부위의 sequence 중 5`-CCCGGGAATTCGCATCGATCGATCGAATGAAGA-ACGCAGC-3`와 5`-CCCGGGATCCTCCGCTTATT-GATATGC-3`를 이용하여 PCR 증폭을 하였을 때 벼도열병균 14개 균주는 동일한 길이의 단일 밴드를 형성하였으며 벼 이외 화본과 식물 도열병균에서는 레드톱 식물로부터 분리한 도열병균만이 나머지 균주보다 38bp가 더 큰 길이를 가진 밴드를 형성하였다. PCR로 증폭된 DNA를 HaeIII와 MspI 제한효소로 절단하였을 때 벼도열병균 레이스간에는 제한효소 절단에 의한 전기영동 밴드 형태 차이를 관찰할 수 없었으나, 벼 이외 화본과 식물 도열병균 12개 균주는 3군으로 구분할 수 있었다. 벼도열병균 90=054와 강아지풀에서 분리한 도열병균 G90-5, 기장에서 분리한 G88-4, 바랭이에서 분리한 G88-5 그리고 레드톱에서 분리한 RT 균주의 ITS II 부위의 DNA 염기서열 비교 분석에 의하면 G88-4와는 다른 HaeIII와 MspI 제한효소 위치를 가지고 있었기에 제한효소 절단에 의한 전기영동 형태가 상이하였다. 또한 RT균주는 HaeIII와 MspI위치가 존재하지 않았다.

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Study on the Genetic Variation of the Mitochondrial DNA in the Beet Armyworm, Spodoptera exigua (H bner), Using PCR-RFLP (PCR-RFLP를 이용한 파방나방 (Spodoptera exigua(H bner)) 미토콘트리아 DNA의 유전변이 연구)

  • 김용균;이명렬;정충렬
    • Korean journal of applied entomology
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    • v.37 no.1
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    • pp.23-30
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    • 1998
  • Restriction fragment length polymorphism (RFLP) of a DNA has been a useful tool for analyzing genetic variation. This research was performed to establish an RFLP analytic method on the mitochondrial DNA (mtDNA) of the beet armyworm, Spodoptera exigua (Hiibner). To do this, total size of the mtDNA was measured and polymerase chain reaction (PCR) primers were selected. Its mitochondrial genome size was ca. 16kb. From a serial PCR test of 29 primers refered to the compilation of Simon et al. (1994), 22 primers were selected to amplify its mtDNA fragments. These primers resulted in short (300-700 bp) or long (1000-2000 bp) DNA products which represented a total or partial sequence of each of CO-I, CO-11, Cyt-B, ND-1, 12s rRNA, 16s rRNA, and some tRNAs. PCR-RFLP was performed in some variable mtDNA regions with 8 kinds of 4bp recognizing restriction enzymes. Different populations from Andong, Kyungsan, and Sunchun did not show any restriction site polymorphisms but had some length variation in certain regions of mtDNA.

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Development of Molecular Detection Marks Using PCR-RFLP Technique for Arkshell (Scapharca broughtonii Schrenck) (피조개, Scapharca broughtonii Schrenck RFLP 마커 개발)

  • Cho Eun Seob;lung Choon Coo;Kim Chul Won;Sohn Sang Cyu
    • Journal of Life Science
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    • v.15 no.6 s.73
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    • pp.879-883
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    • 2005
  • This study was differentiated between Korea and China arkshells using PCR-aided RFLP method which could identify the variation for inter-and intra-species of arkshell (Scapharca broughtonii Schrenck) at the level of DNA. The DNA fragment patterns were compared after digesting gene of mitochondrial 16S rDNA with 8 kinds of restriction enzymes. A 720 bp DNA fragment corresponding to 16S rDNA gene was amplified by PCR with primers ArkF-3 and ArkR-3. PCR products were cut by restriction enzymes (Pvull, BamHI, Hinfl, HaeIII, EcoRI, RsaI, Ksp221, and BstX21), and RFLP pattern was studied. A unique 275 bp DNA band was observed in the samples from Dukyang, Gamak, Namhae, Jinhae, and Taean in Korea when treated by Hinfl, but Chinese arkshell did not show. Treatment of HaeIII could discriminate the sample of Namhae and Jinhae from Dukyang/Gamak/Taean, as well as Korean and Chinese arkshell based on a 700 bp. However, PuvII, BamHI, EcoRI, RsaI, Ksp221, and BstX21 showed the same of 700 bp band in Korean and Chinese arkshell. The phylogenetic tree inferred from PCR-RFLP pattern comparsion in Korean arkshell was different that the distance between Dukyang/Gamak/Taean and Namhae/Jinhae was approximately 7. In particular, the distance between Korean and Chinese arkshell was 25. Consequently, HinfI and HaeIII played an important role in a reliable molecular tool for rapid discriminating Korean and Chinese arkshell, as well as a intra-species in Korea.

Genetic Stock Identification of Spotted Flounder, Verasper variegatus from Yeocheun, Korea (범가자미에 대한 유전학적 동정)

  • KIM Kyung Kil;KIM Yoon;NAM Yoon Kwan;KIM Dong Soo
    • Journal of Aquaculture
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    • v.6 no.3
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    • pp.221-233
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    • 1993
  • Cell size, DNA content, chromosome and PCR-based mitochondrial 12S rRNA gene analyses were conducted to obtain basic informations for genetic stock identification of spotted flounder (Verasper variegatus) from Yeocheun, Korea. The mean erythrocytic and nuclear volumes of spotted flounder were $211.10{\mu}m^3$ and $23.03{\mu}m^3$, respectively. The haploid DNA content of this species was 0.79 pg/cell which correspond to $46.5\%$ of carp and to $22.6\%$ of mammals. Spotted flounder had the 2n = 46 acrocentric chromosomes but no heteromorphic sex chromosomes was found. Mitochondrial DNA gene for 12S ribosomal RNA was amplified by polymerase chain reaction (PCR) and the PCR products were subjected to digestion with 15 restriction endonucleases. Restriction enzyme analyses revealed that Ava I, Mae II, Sma I and Xba I had one restriction site in the mitochondrial 12S rRNA gene segment of spotted flounder, while Mae I had two. Segments of 12S rRNA gene from mitochondria in spotted flounder were sequenced and compared with channel catfish and human as controls. The 12S rRNA gene of this species was more similar to that of channel catfish than to human's.

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Phylogenetic Analysis of Agaricus blazei and Related Taxa by Comparing the Sequences of Internal Transcribed Spacers and 5.8S rDNA (Internal Transcribed Spacer와 5.8S ribosomal DNA의 염기서열 분석에 의한 Agaricus blazei와 근연종에 대한 계통분류학적인 연구)

  • 김기영;하명규;이태호;이재동
    • Korean Journal of Microbiology
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    • v.35 no.3
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    • pp.180-184
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    • 1999
  • Molecular spslemaucs of Agaricus species was investigated on the base of the sequences of the internal transcribed spaceriITS) regions in ribosomal DNA (rDNA). The sequences of the ITS region in 5 species and two group of Agaricus genus were resolved. In the phylogenetic trees. the species generally divided inlo two subclusters, refered to here as the group I and group 11. The group I consisted of Agaricus blazei ATCC 76739, Agarictrs blazei species cultivated in Korean hmings. Ago/-icus anmensis IMSNU 32049 and Agaricus can~pestris VPI-OKM 25665. Between Agaricus blazei NCC 76739 and the Agaricus blazei species cultivated in Korean farmings had the variation in lhe 5 nucleotide on the ITS regions. These varieties were presumed the variation by the geographic and cultivated conditions. In addition the subgroup of group I was formed by Agaricus arvensis LMSNU 32049 and Agaricus carnpests VPI-OKM 25665. The group IT included Agnrictrs bispoms CH 3004 and Agaricus pocillotor DUKE-J 173.

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Cloning and Organization of the Ribosomal RNA Genes of the Mushroom Trichloma matsutake

  • Hwang, Seon-Kap;Kim, Jong-Guk
    • Journal of Microbiology and Biotechnology
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    • v.5 no.4
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    • pp.194-199
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    • 1995
  • A portion (7.4 kb) of ribosomal DNA tandem repeat unit from a genome of the mushroom T. matsutake has been cloned. A 1.75 kb EcoRI fragment was cloned first using S. cerevisiae 255 rRNA gene as a probe, and this was then used for further cloning. A chromosomal walking experiment was carried out and the upstream region of the 1.75 kb fragment was cloned using SmaI/BamHI enzyme, the size was estimated to be 5.2 kb in length. Part of the downstream region of the 1.75 kb fragment was also cloned using XbaI/BamHI enzymes. Restriction enzyme maps of three cloned DNA fragments were constructed. Northern hybridization, using total RNA of T. matsutake, and the restriction fragments of three cloned DNAs as probes, revealed that all four ribosomal RNA genes (large subunit[LSU], small subunit [SSU], 5.85 and 5S rRNA genes) are present in the cloned region. The gene organization of the rDNA are regarded as an intergenic spacer [IGS]2 (partial) - SSU rRNA - internal transcribed spacer [ITS]1 - 5.8S rRNA - ITS2 - LSU rRNA - IGS1 -5S rRNA - IG52 (partial).

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Application of the 18S Ribosomal DNA (rDNA) PCR-RFLP Technique for the Differential Diagnosis of Anisakidosis (고래회충유충증 감별 진단을 위한 18S ribosomal DNA (rDNA) PCR-RFLP 법 적용)

  • Kim, Sun-Mee;Cho, Min-Kyung;Yu, Hak-Sun;Cha, Hee-Jae;Ock, Mee-Sun
    • Journal of Life Science
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    • v.19 no.9
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    • pp.1328-1332
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    • 2009
  • Anisakidosis is caused by anisakid nematodes (family Anisakidae) larvae which can cause not only direct tissue damage but also a severe allergic response related to excretory-secretion products. Lots of different species of anisakid larvae, including Anisakis simplex, Contracaecum, Goezia, Pseudoterranova, and Hysterothylacium, cause the anisakidosis. But it is difficult to diagnosis the species of larvae since the morphologies of larval anisakid nematodes are almost indistinguishable. In order to diagnosis the differential infections of larval anisakid nematodes, polymerase chain reaction - restriction fragment length polymorphism (PCR-RFLP) of 18S rDNA - was conducted. Three major species of anisakid larvae including A. simplex, C.ontracaecum spp, and Goezia spp. were collected from mackerel (Scomber japonicus), mullet (Mugil cephalus), founder (Paralichthys olivaceus), eel (Astroconger myriaster) and red sea bream (Pagrus major). PCR amplified 18S rDNA from each species of anisakid larvae was digested with eight restriction enzymes including Taq I, Hinf I, Hha I, Alu I, Dde I, Hae III, Sau96 I, and Sau3A I. The original sizes of PCR amplified 18S rDNA were 2.0Kb in both anisakid larvaes and Goezia. Restrction enzymes including Hinf 1, Alu 1, Hha I, Dde 1 and Hae III cut differently and distinguished the A. simplex and Contracaecum type C'. However, Contracaecum type A showed two different restriction enzyme cutting patterns by Taq 1, Hinf I, Alu 1, and Dde 1. One of the patterns was the same as those of A. simplex, Contracaecum type C' and Goezia and the other was unique. These results suggest that PCR-RFLP pattern by Hinf 1, Alu 1, Hae I, Dde 1 and Hae III can be applied to differential diagnosis of human infection with A. simplex and Contracaecum type C'. Contracaecum type A needs further study of classification by morphological characteristics and genetic analysis.

Nucleotide Sequences of an Aphid ribosomal RNA Unit (진딧물의 전 ribosomal RNA 염기배열)

  • Kwon, Tae-Young;An, Seung-Lak;Song, Cheol;Park, Jong-Kyun;Kim, Young-Sub;Hwang, Jae-Sam;Kwon, O-Yu
    • Journal of Life Science
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    • v.8 no.1
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    • pp.32-39
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    • 1998
  • The length and G/C concent of regions of an aphid rDNA unit that spans 13,061bo with 59% G/C content. flolowing belowing below are the those results, 5’ETS is 843bp in length with 69% G/C content, 18S is 2,469bp in length with 59% G/C content, ITS I is 229bp in length with 70% G/C content, 5.8S is 160bp in length with 63% G/C content, ITS II is 325bp in length with 70% G/C content, 28S is 4, 147bp in length with 60% G/C content, IGS is 4,888bp in length with 55% G/C content.

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