• Title/Summary/Keyword: 28S rDNA

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ITS Primers with Enhanced Specificity to Detect the Ectomycorrhizal Fungi in the Roots of Wood Plants

  • Kim, Dong-Hun;Chung, Hung-Chae;Ohga, Shoji;Lee, Sang-Sun
    • Mycobiology
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    • v.31 no.1
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    • pp.23-31
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    • 2003
  • With universal primer ITS1-F, the specific DHJ2 primer was developed to detect the Ectomycorrhizal(ECM) root tips in soil and to identify the species of ECM fungi, as based on DNA sequences of rDNA stored in GeneBank of NCBI. This primer was designed with the common sites of rDNA of Amanita and Boletus, and was also designed with several DNA programs provided by NCBI. The DNA fragments synthesized by PCR were calculated to be 1,000 to 1,200 bps of DNA located to 18s to 28s rDNA to contain two variable sites of ITS, indicating much diversities for specific species or ecotypes of ECM fungi. The primer DHJ2 reacted with the genomic DNA's extracted from the tissues of basidiocarp at the rate of 73 of 80 fungi collected produced single bands with a 1,100 bps length. The DNA fragment synthesized with the genomic DNA that extracted from eight ECM tips of Pinus densiflora was confirmed and analysized to the rDNAs of ECM in full sequences, and informed to be a ECM fungal species in the forest.

Secondary Structure of the Ribosomal Internal Transcribed Spacer (ITS) Region of Hypsizygus marmoreus (느티만가닥버섯의 ITS (internal transcribed spacer) 영역의 2차구조 분석)

  • Woo, Ju-Ri;Yoon, Hyeokjun;You, Young-Hyun;Lee, Chang-Yun;Kong, Won-Sik;Kim, Jong-Guk
    • Journal of Life Science
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    • v.23 no.10
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    • pp.1260-1266
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    • 2013
  • The ribosomal DNA (rDNA) clusters of Hypsizygus marmoreus 3-10 and H. marmoreus 1-1 were analyzed in this study. The small subunit (SSU) and intergenic spacer 2 (IGS 2) was partially sequenced. The internal transcribed spacer 1 (ITS 1), 5.8S, internal transcribed spacer 2 (ITS 2), large subunit (LSU), intergenic spacer 1 (IGS 1), and 5S were completely sequenced. The rDNA clusters of H. marmoreus 3-10 and H. marmoreus 1-1 were 7,049 bp in length. The sequence of SSU rDNA, which corresponded to 18S rDNA, was 1,796 bp in length, and the sequence of LSU rDNA, which corresponded to 28S rDNA, was 3,348 bp in length. The ITS region that variable region and IGS region that non-transcribed spacer was 462 bp and 1,290 bp in length. The sequence of 5.8S rDNA and 5S rDNA was 153 bp and 43 bp in length, respectively. The 17 bp of the rDNA cluster in the H. marmoreus 3-10 strain was different to that in the H. marmoreus 1-1 strain, with 2 bp in the SSU, 3 bp in the ITS, 9 bp in the LSU, and 3 bp in the IGS. The analysis of the secondary structure revealed that the ITS regions of H. marmoreus 3-10 and H. marmoreus 1-1 have five stem-loop structures. Interestingly, among these structures, one different nucleotide sequence resulted in a different secondary structure in stem-loop V.

Flow Cytometric and Cytogenetic Studies in Rhychocypris oxycephalus and R. steindachneri (버들치, Rhynchocypris oxycephalus와 버들개, R. steindachneri의 Flow Cytometry 및 세포유전학적 분석)

  • Park, In-Seok;Choi, Youn;Kim, Yong-Ho;Nam, Yoon-Kwon;Kim, Dong-Soo
    • Journal of Aquaculture
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    • v.13 no.3
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    • pp.193-196
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    • 2000
  • Rhynchocypris oxycephalus and R. steindachneri show very similar karyotypes: 2n=50(EN=90), consisting of 12 metacentics, 28 submetacentrics and 10 acrocentrics with a gradual decrease in chromosome size, but with significant differences in nuclear DNA content of 2.64 and 2.52 pg/nucleus, respectively (P<0.05). Although the erythrocyte measurement and parameters of two species were similar, R. oxycephalus erythrocyte number was lower than that of R. steindachneri. Mode in karyological evolution within the genus Rhychocypris shows an increase of nuclear DNA without apparent changes in karyotype and erhthrocyte size.

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Intrageneric Relationships of Trichoderma Based on Internal Transcribed Spacers and 5.8S rDNA Nucleotide Sequences

  • Kim, Gi-Young;Lee, Goang-Jae;Ha, Myung-Gyu;Lee, Tae-Ho;Lee, Jae-Dong
    • Mycobiology
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    • v.28 no.1
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    • pp.11-16
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    • 2000
  • The nucleotide sequences of the internal transcribed spacer (ITS) regions of the ribosomal DNA including the 5.8S ribosomal RNA gene (rDNA) have been determined for 11 species in order to analyze their intrageneric relationships. The total length of these sequences ranged from 530 nucleotides for Trichoderma reesei KCTC 1286 to 553 nucleotide for Trichoderma koningii IAM 12534. Generally speaking, the length of ITS1 region was about 30 nucleotides longer than that of the ITS2 region. Also, the sequences of 5.8S rDNA were more conserved in length and variation than those of ITS regions. Although the variable ITS sequences were often ambiguously aligned, the conserved sites were also found. Thus, a neighbor-joining tree was constructed using the full sequence data of the ITS regions and the 5.8S rDNA. The Trichoderma genus used to be grouped on the basis of the morphological features and especially the shape of phialides needs to be reexamined. The phylogenetic tree displayed the presence of monophylogeny in the species of Trichoderma. Therefore, it was difficult to distinguish the intrageneric relationships in the Trichoderma genus.

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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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Identification of the Orchid Mycorrhizal Fungi Isolated from the Roots of Korean Native Orchid

  • Lee, Sang-Sun;You, Jae-Hyung
    • Mycobiology
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    • v.28 no.1
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    • pp.17-26
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    • 2000
  • The orchid symbiotic fungi were isolated from the roots of Korean native orchid (Cymbidium goeringii) collected and Chinese orchid (C. sinense) obtained from greenhouses. They were identified as a species of Rhizoctonia, based on the sequences of 18r rDNA, the microscopic observations of mycelia, and the symbiotic relationships with commercial orchids. The isolate collected from Chinese orchids was revealed to be a species of Ceratobasidium endophytica, and to be different from the other isolates at the thickness of the mycelia stained in the root cells of Korean native orchids. The other isolates collected from the Korean native orchids were considered to be a species of Tulsanella repens (anamorphic: Epulorhiza repens) or its related one. The physiologic or microscopic variations were oftenly observed among them, but the tendency of grouping these in the 18s rDNA sequences were observed to be consistent with those of the localities collected. The further taxonomical segregating for Korean symbiotic fungi was not made because the information concerned were limited in this moment, but was recognized as based on the sequences of 18s DNA.

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Comparative Analysis of the Community of Culturable Bacteria Associated with Sponges, Spirastrella abata and Spirastrella panis by 16S rDNA-RFLP (16S rDNA-RFLP에 의한 Spirastrella abata와 Spirastrella panis 해면에 서식하는 배양가능한 공생세균 군집의 비교)

  • Cho, Hyun-Hee;Park, Jin-Sook
    • Korean Journal of Microbiology
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    • v.45 no.2
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    • pp.155-162
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    • 2009
  • A cultivation-based approach was employed to compare the culturable bacterial diversity associated with two phylogenetically closely related marine sponges, Spirastrella abata and Spirastrella panis, which have geologically overlapping distribution patterns. The bacteria associated with sponge were cultivated using MA medium supplemented with 3% sponge extracts. Community structures of the culturable bacteria of the two sponge species were analyzed with PCR-RFLP (restriction fragment length polymorphism) based on 16S rDNA sequences. The RFLP fingerprinting of 16S rDNA digested with HaeIII and MspI, revealed 24 independent RFLP types, in which 1-5 representative strains from each type were partially sequenced. The sequence analysis showed >98.4% similarity to known bacterial species in public databases. Overall, the microbial populations of two sponges investigated were found to be the members of the classes; Alphaproteobacteria, Gammaproteobacteria, Firmicutes, and Actinobacteria. The Alphaproteobacteria were predominant in the bacterial communities of the two sponges. Gammaproteobacteria represented 38.5% of bacterial community in S. abata. Whereas only 1.6% of this class was present in S. panis. Bacillus species were dominat in S. panis. Bacillus species were found to be 44.3% of bacterial species in S. panis, while they were only 9.7% in S. abata. It is interesting to note that Planococcus maritimus (8.1%, phylum Firmicutes) and Psychrobacter nivimaris (28.9%, phylum Gammaproteobacteria) were found only in S. abata. This result revealed that profiles of bacterial communities from the sponges with a close phylogenetic relationship were highly species-specific.

Occurrence of Plant Parasitic Nematodes in Chrysanthemum and ITS and D3-28S rDNA Characterization of Pratylenchus spp. (국화재배지의 식물기생선충 분포조사 및 뿌리썩이선층의 ITS와 D3-28S rDNA 특성조사)

  • Han, Hye-Rim;Lee, Jae-Kook;Choi, Dong-Ro;Han, Man-Jong;Park, Byeong-Yong
    • Korean journal of applied entomology
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    • v.45 no.3 s.144
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    • pp.293-299
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    • 2006
  • A survey was conducted to find out the major plant parasitic nematode in Chrysanthemum morifolium fields in Korea from May to June in 2005. A genus of Pratylenchus was determined as the most important plant parasitic nematode based on analysis of total 50 samples from 8 cities of chrysanthemum field. Pratylenchus showed 86% occurrence rate and average numbered 1,095 per 200cc soils and 1g root. Five Pratylenchus isolates, 'Muan', 'Masan', 'Tean', 'Gumi', 'Jeongup', were selected for the molecular identification of the species of Pratylenchus, and ITS and D3-28S ribosomal DNA were amplified by PCR. For the ITS, only 'Muan' isolate was differentiated by total 1 kb PCR amplification, which was 200 bp larger than all the other isolates. There was no size variation in amplified D3-28S rDNA and all isolate represented approximately 320 bp of PCR product. Sequence data of D3-28S rDNA were analysed by MegAlign program in DNASTAR software and phylogenetic tree was constructed. Sequence homology was 100% between 'Gumi' isolate and 'Tean' isolate and 'Jeongup' isolate was also close to these isolates by 99.7% sequence homology. 'Gumi', 'Tean' group and 'Jeongup' isolate were determined to be closely related to Pratylenchus vulnus by 96.7% and 96.3% similarity in respectively. D3 sequence of 'Masan' isolate was 100% identical to P. penetrans, and 'Muan' isolate showed 99.7% similarity to P. brachyurus. This result was congruent with the branch divergence pattern shown in phylogenetic tree.

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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Comparison of the Phylogenetic Diversity of Humus Forest Soil Bacterial Populations via Different Direct DNA Extyaction Methods (DNA 직접추출법에 따른 산림토양 부식층 내 세균군집의 계통학적 다양성 비교)

  • Son, Hee-Seong;Han, Song-Ih;Whang, Kyung-Sook
    • Korean Journal of Microbiology
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    • v.43 no.3
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    • pp.210-216
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    • 2007
  • The principal objective of this study was to analyze 16S rDNA-ARDRA of the humus forest soil via an improved manual method and an ISOIL kit on the basis of the UPGMA clustering of the 16S rDNA combined profile, 44 ARDRA clusters of 76 clones via the ISOIL kit method and 45 ARDRA clusters of 136 clones via the improved manual method. On the basis of the 16S rDNA sequences, 44 clones from the ARDRA clusters by the ISOIL kit were classified into 3 phyla : ${\alpha}-,\;{\beta}-,\;{\gamma}-,\;{\delta}-Proteobacteria$, Acidobacteria and Actinobacteria. Using the improved manual method, the specimens were classified into 6 phyla : the ${\alpha}-,\;{\beta}-,\;{\gamma}-,\;{\delta}-Proteobacteria$, Acidobacteria, Bacteroides, Verrucomicrobia, Planctomycetes and Gemmatomonadetes. As a result, the modified manual method indicated greater phylogenetic diversity than was detected by the ISOIL kit. Approximately 40 percent of the total clones were identified as ${\alpha}-Proteobacteria$ and 30 percent of the total clones were ${\gamma}-Proteobacteria$ and assigned to dominant phylogenetic groups using the ISOIL kit. Using the modified manual method, 41 percent of the total clones were identified as Acidobacteria and 28 percent of total clones were identified as ${\alpha}-proteobacteria$ and assigned to dominant phylogenetic groups.