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느티만가닥버섯의 ITS (internal transcribed spacer) 영역의 2차구조 분석
우주리(Ju-Ri Woo),윤혁준(Hyeokjun Yoon),유영현(Young-Hyun You),이창윤(Chang-Yun Lee),공원식(Won-Sik Kong),김종국(Jong-Guk Kim) 한국생명과학회 2013 생명과학회지 Vol.23 No.10
본 연구에서는 H. marmoreus 3-10균주와 H. marmoreus 1-1균주의 ribosomal DNA (rDNA) cluster의 분석이 수행되었다. Small subunit (SSU)와 intergenic spacer 2 (IGS 2)는 부분적으로 염기서열이 결정되었고, internal transcribed spacer 1 (ITS 1), 5.8S, internal transcribed spacer 2 (ITS 2), large subunit (LSU), intergenic spacer 1 (IGS 1), 5S는 완전하게 염기서열이 결정 되었다. 팽이버섯 H. marmoreus 3-10균주와 H. marmoreus 1-1균주의 rDNA cluster는 총 7,049 bp로 결정되었다. SSU은 1,796 bp, ITS1은 229 bp, 5.8S은 153 bp, ITS2는 223 bp, LSU은 3,348 bp, IGS1은 390 bp, IGS2은 900 bp로 염기서열이 분석되었다. 결정된 rDNA cluster의 총 7,049 bp 중에서 17 bp가 다름이 확인되었고, 각각 SSU (2 bp), ITS (3 bp), LSU (9 bp), IGS (3 bp)에서 차이를 확인하였다. ITS regions의 2차 구조 결과 5개의 stem-loop가 있음이 드러났다. 흥미롭게도, 이들 stem-loop 사이에서 stem-loopⅤ에서 한 개의 상이한 염기가 다른 2차 구조를 나타냄을 확인하였다. 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 nontranscribed 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.
Flammulina velutipe의 국내 균주와 외래 균주 간의 ITS region을 이용한 계통학적 유연관계 분석
Gwang-Rip Hwang(황광립),Ju-Ri Woo(우주리),Hyeokjun Yoon(윤혁준),Chang-Yun Lee(이창윤),Sang-Han Lee(이상한),Won-Sik Kong(공원식),Jong-Guk Kim(김종국) 한국생명과학회 2012 생명과학회지 Vol.22 No.1
본 연구는 팽이버섯(Flammulina velutipes)의 국내 균주와 외래 균주간의 유전적 유연관계를 조사하기 위하여 수행되었으며, 계통수 측정 결과 3개 그룹으로 나눠짐을 확인하였다. 20개 F. velutipes 균주들의 ITS region 염기서열을 확보하였으며, 이들 서열을 바탕으로 multiple alignment를 보았으며, Neighbor-joining method를 이용하여 계통수를 작성하였으며, 2개 그룹으로 나눠짐을 확인하였다. 또한 F. velutipes 4154 균주의 rDNA-cluster를 최초로 분석한 결과, 총 10,974 bp임을 밝혔다. SSU는 1,806 bp, ITS region은 553 bp의 염기배열이 결정되었다. ITS 1 부분은 245 bp이고 ITS 2는 308 bp였으며, LSU에 해당되는 염기서열은 3,402 bp, IGS 1은 1,400 bp, 5S는 83 bp, IGS 2는 3,571 bp임을 확인하였다. This study was carried out to investigate the genetic relationship of Flammulina velutipes with other species. The ribosomal DNA cluster containing 4 rRNA genes from F. velutipes 4154 were sequenced. The length of the rDNA cluster sequence was estimated at 7,403 bp long and consisted of 1,806 bp of SSU rDNA, 245 bp of ITS 1 region, 159 bp of 5.8S rDNA, 308 bp of ITS 2 region, 3,402 bp of LSU rDNA, 1,400 bp of IGS 1 region, and 83 bp of 5S rDNA. The F. velutipes 4154 genes were contained in the rDNA cluster of F. velutipes in the order of SSU rDNA - ITS 1 - 5.8S rDNA - ITS 2 - LSU rDNA - IGS 1 - 5S rDNA. The phylogenetic relationships of 20 strains of Tricholomataceae and Physalacriaceae were analyzed by conducting distance analysis using the Neighbor-joining (NJ) method. The 20 strains used in this study were divided into three groups and the strains of the genus Flammulina were related very closely to strains of Physalacria bambusae.
Myung Soo Park,Geon Sik Seo,Kyung Sook Bae,유승헌 한국식물병리학회 2005 Plant Pathology Journal Vol.21 No.3
Molecular profiles of PCR-RFLP and sequence analysis of internal transcribed spacer (ITS) regions of rDNA were compared between morphologically distinguishable species of Trichoderma isolated from substrates of oyster mushroom in Korea, T. atroviride, T. citrinoviride,T. harzianum, T. longibrachiatum, T. virens, and two unidentified species, Trichoderma sp. 1 and 2. PCRRFLP analysis divided the Trichoderma spp. into six RFLP groups, A, B, C, D, E, and F. The RFLP groups were generally agreed with described morphological species, except that the RFLP group A containing the two unidentified species. A neighbor-joining tree based on ITS sequences well supported RFLP groups observed by RFLP analysis of ITS regions of rDNA.Additionally, the two unidentified species, Trichoderma sp. 1 and 2, which could not be distinguished by PCRRFLP analysis, were separated in sequence analysis of ITS regions of rDNA.
Park, Myung-Soo,Seo, Geon-Sik,Bae, Kyung-Sook,Yu, Seung-Hun The Korean Society of Plant Pathology 2005 Plant Pathology Journal Vol.21 No.3
Molecular profIles of PCR-RFLP and sequence analysis of internal transcribed spacer (ITS) regions of rDNA were compared between morphologically distinguishable species of Trichoderma isolated from substrates of oyster mushroom in Korea, T. atroviride, T. citrinoviride, T. harzianum, T. longibrachiatum, T. virens, and two unidentified species, Trichoderma sp. 1 and 2. PCRRFLP analysis divided the Trichoderma spp. into six RFLP groups, A, B, C, D, E, and F. The RFLP groups were generally agreed with described morphological species, except that the RFLP group A containing the two unidentified species. A neighbor-joining tree based on ITS sequences well supported RFLP groups observed by RFLP analysis of ITS regions of rDNA. Additionally, the two unidentified species, Trichoderma sp. 1 and 2, which could not be distinguished by PCRRFLP analysis, were separated in sequence analysis of ITS regions of rDNA.
Characteristic evaluation of collected strains of Hypsizygus marmoreus based on ITS rDNA sequence
Youn-Keol Nam,Youn-Lee Oh,Won-Sik Kong,Kab-Yeul Jang,Pyung-Gyun Shin,Min-Ji Oh,Eun-Seon Kim,Sung-I Woo,Chang-Duck Koo 한국버섯학회 2015 버섯 Vol.19 No.1
The aim of this study was to analyze the genetic diversity of collected strains of Hypsizygus marmoreus based on their rDNA ITS sequences. The size of ITS rDNA regions of H. marmoreus strains, collected form various regions. A phylogenetic trees based on the ITS region revealed that the strains could be classified into 4 different groups including Villosiclava virens, Hypsizygus marmoreus, Lepista irina, Lyophyllum Decastes, Lyophyllum shimeji, Pleurotus floridanus.
Characteristic evaluation of collected strains of Hypsizygus marmoreus based on ITS rDNA sequence
Youn-Keol Nam,Youn-Lee Oh,Won-Sik Kong,Kab-Yeul Jang,Pyung-Gyun Shin,Min-Ji Oh,Eun-Seon Kim,Sung-I Woo,Chang-Duck Koo 한국버섯학회 2015 버섯 Vol.19 No.2
The aim of this study was to analyze the genetic diversity of collected strains of Hypsizygus marmoreus based on their rDNA ITS sequences. The size of ITS rDNA regions of H. marmoreus strains, collected form various regions. A phylogenetic trees based on the ITS region revealed that the strains could be classified into 4 different groups including Villosiclava virens, Hypsizygus marmoreus, Lepista irina, Lyophyllum Decastes, Lyophyllum shimeji, Pleurotus floridanus.
ITS 분석을 이용한 노루궁뎅이버섯 수집균주의 계통분류
문지원,이찬중,정종천,서장선,공원식 한국버섯학회 2014 한국버섯학회지 Vol.12 No.4
The aim of this study was to analyze the genetic diversity of Hericium species based on their rDNA ITS sequences. Hericium species were collected from various regions and the size of the ITS rRNA gene regions from different Hericium species varied from 450 to 500 bp. A phylogenetic trees based on the ITS region revealed that Hericium species could be classified into 4 different groups, H. erinaceus, H. coralloide, H. alpestre, H. americanum. Among them, ASI 48015 and ASI 48016 was identified as Sprassis and Lentinula genus, respectively, based on blast searches using their rDNA ITS sequences.
도열병균(Magnaporthe grisea)의 Ribosomal DNA의 ITS II 부위 핵산 염기서열을 이용한 균주간 근연관계 비교
배신철,이신우,이인구,예완해,류진창 한국식물병리학회 1996 Plant Pathology Journal Vol.12 No.1
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.