• Mycobiology
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• 제28권1호
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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.

• The Plant Pathology Journal
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• 제40권2호
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• pp.171-191
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• 2024

Identification of Helicotylenchus species is very challenging due to phenotypic plasticity and existence of cryptic species complexes. Recently, the use of rDNA barcodes has proven to be useful for identification of Helicotylenchus. Molecular markers are a quick diagnostic tool and are crucial for discriminating related species and resolving cryptic species complexes within this speciose genus. However, DNA barcoding is not an error-free approach. The public databases appear to be marred by incorrect sequences, arising from sequencing errors, mislabeling, and misidentifications. Herein, we provide a comprehensive analysis of the newly obtained, and published DNA sequences of Helicotylenchus, revealing the potential faults in the available DNA barcodes. A total of 97 sequences (25 nearly full-length 18S-rRNA, 12 partial 28S-rRNA, 16 partial internal transcribed spacer [ITS]-rRNA, and 44 partial cytochrome c oxidase subunit I [COI] gene sequences) were newly obtained in the present study. Phylogenetic relationships between species are given as inferred from the analyses of 103 sequences of 18S-rRNA, 469 sequences of 28S-rRNA, 183 sequences of ITS-rRNA, and 63 sequences of COI. Remarks on suggested corrections of published accessions in GenBank database are given. Additionally, COI gene sequences of H. dihystera, H. asiaticus and the contentious H. microlobus are provided herein for the first time. Similar to rDNA gene analyses, the COI sequences support the genetic distinctness and validity of H. microlobus. DNA barcodes from type material are needed for resolving the taxonomic status of the unresolved taxonomic groups within the genus.

• 한국균학회지
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• 제27권2호통권89호
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• pp.124-131
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• 1999

본 실험은 진흙버섯류 7종 15균주에 대한 5.85 rDNA와 ITS 부위의 염기서열을 비교 분석함으로서 종간 및 종내의 유연관계를 조사하였다. 5.8S rDNA와 ITS 부위를 증폭하고자 18S rDNA의 3'말단 부위와 28S rDNA의 5'말단 부위에 두 개의 primer를 이용하여 PCR증폭을 행하였다. 5.8S rDNA와 ITS 부위를 증폭하여 염기서열을 비교 분석한 결과 본 실험에 공시된 Phellinus속의 제균종은 크게 4개의 cluster를 형성하였다. 첫 번째 cluster는 Phellinus hartigii IMSNU 32041, Phellinus robustus IMSNU 32068로 이루어졌고, 두 번째 cluster는 Phellinus linteus KCTC 6190, IMSNU 31014, DGUM 25003, DGUM 25004, Phellinus sp. DGUM 25007, Namsan No. 1과 Phellinus weirianus IMSNU 32021, 세 번째 cluster는 Phellinus laevigatus KCTC 6229, KCTC 6230과 Phellinus igniarius KCTC 6227, KCTC 6228로 이루어졌으며, Phellinus chrysoloma KCTC 6225와 KCTC 6226이 마지막 cluster를 형성하였다. 결과적으로 ITS 염기서열의 결과만으로 볼 때 Phellinus linteus와 Phellinus weirianus는 명확하게 종 단위의 개념을 정립할 수 없었다. 따라서 정확한 분류를 위해 생리학적, 분자생물학적 인 분류방법이 첨가되어야 하며, type strain에 대한 ITS 염기서얼도 결정되어야 한다. Phellinus속의 균들에서는 ITS2부위에 비해 ITS1부위의 변이율이 높았다. ITS 염기서열은 종 구분에 유용한 도구이며, 다른 균종들과 비교해 보았을 때 Phellinus linteus와 Phellinus weirianus에서만 ITS1 부위에서 특이적인 염기서열을 가지고 있었다.

• 생명과학회지
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• 제22권8호
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• pp.1120-1125
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• 2012

국내에 자생 중인 큰엉겅퀴(Cirsium pendulum)를 강원도의 홍천, 원주, 평창, 양양 및 경기도 가평과 충청북도의 충주에서 채취하고, 고려엉겅퀴(Cirsium setidens)를 강원도의 태백 및 경상북도의 봉화에서 채취하였다. 채취된 식물들의 genomic DNA를 분리하여서 18S rDNA, ITS1, 5.8S rDNA, ITS2 및 28S rDNA의 일부를 증폭하고, 그 염기서열을 분석하였다. 이렇게 얻어진 염기서열을 GenBank에 등록하고, 서로 비교해 보았다. 그 결과 큰엉겅퀴는 6개체 모두에서 18S rDNA 및 5.8S rDNA의 염기서열은 서로 완전히 일치하고 있으나, ITS1과 ITS2의 염기서열에서는 약간의 차이를 보였다. 고려엉겅퀴의 경우에는 18S rDNA, ITS1 및 ITS2에서 2개체가 서로 비교적 큰 차이를 보였다. 일본의 홋카이도에서 채취된 큰엉겅퀴와 중국의 안휘성에서 채취된 엉겅퀴(Cirsium japonicum)를 포함하여서 ITS1과 ITS2 염기서열을 비교한 결과, 엉겅퀴, 큰엉겅퀴, 고려엉겅퀴는 확연하게 서로 다른 그룹을 형성하는 것으로 나타났다. 또한 채취된 큰엉겅퀴 및 고려엉겅퀴들의 silymarin 함량을 분석해 본 결과, 모두에서 그 함량이 2 mg/ml가 넘는 것으로 나타났다. 따라서 엉겅퀴뿐만 아니라 큰엉겅퀴나 고려엉겅퀴도 여러 가지 약리작용을 가진 것으로 보고된 silymarin을 상당히 높은 농도로 함유하고 있는 것으로 나타났다.

• Mycobiology
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• 제29권3호
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• pp.121-131
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• 2001

This study was carried out to identify the phylogenetic relationships among several caterpillar fungi by comparing the sequences of internal transcribed spacer regions(ITS1 and ITS2) and 5.8S ribosomal DNA(rDNA) repeat unit. The sequences of ITS1, ITS2, and the 5.8S rDNA from 10 strains of Cordyceps species, 12 strains of Paecilomyces, 3 strains of Beauveria, 2 strains of Metarhizium and 1 strains of Hirsutella were amplified, determined and compared with the previously known Cordyceps species. 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 could be found. In the phylogenetic tree, the species generally divided into three clusters, supported by their morphology and/or host ranges. The 5.8S rDNA and TTS1 sequences among 10 species of Cordyceps militaris were identical and only one base pair in ITS2 sequence was different. Cordyceps sinensis and Cordyceps ophioglossoides were also clearly different, although they belonged to the same cluster. The Geniank database search of species revealed sister taxa of an entomogenous fungus. Metarhizium was used as an putgroup in all taxa.

• 한국약용작물학회지
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• 제12권1호
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• pp.60-66
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• 2004

한국산 옻나무속 6종에 대하여 분자식물학적 방법으로 계통유연관계를 확인하기 위하여, nrDNA의 ITS 구간과 cpDNA rbcL 염기서열을 사용하여 계통분석한 결과 ITS 1의 길이는 $246{\sim}253\;bp$이었고, ITS 2는 $234{\sim}244\;bp$이었다. ITS 1의 길이는 Rhus sylvestris와 R. succedanea에서 246 bp로 가장 작았으며, R. verniciflua에서 253 bp로 가장 긴 것으로 나타났다. ITS 2의 길이는 R. verniciflua가 234 bp로 가장 짧았으며, R. trichocarpr가 244 bp로 가장 길게 나타났다. 이들 분류군의 G+C Content는 ITS 1에서는 $58.0{\sim}68.13%$의 범위를 나타냈고, ITS 2에서는 $59.75{\sim}68.46%$로 나타나 두 구간이 비슷한 비율을 보이고 있었다. ITS 1에서의 G+C content는 R. sylvestris가 58.0%로 가장 낮았으며, 가장 높은 값은 R. ambigua가 68.13%로 확인되었다. ITS 2에서는 외군인 Cotinus coggygria가 59.75%로 가장 낮았으며, R. ambigua가 68.46%로 가장 높게 나타났다. 한국산 옻나무 속에서 ITS 염기서열은 일반적으로 피자식물이 갖는 G+C content 범위 안에 포함되는 것으로 확인되었다. 한편, rbcL의 길이는 1,428 bp로 모든 종에서 동일하였다. 또한 rbcL의 G+C content는 $43.56%{\sim}43.77%$로 나타나 종간에 거의 차이가 없음을 확인하였다. 연구결과 rbcL gene은 옻나무속의 종간 계통유연관계를 해석하는데 유용하지 않았으며, ITS 1 구간의 염기서열 변이는 향후 옻나무속을 분류할 때 신속하게 분류할 수 있는 분류 marker로 이용할 수 있다고 판단되었다.

• Molecules and Cells
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• 제23권1호
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• pp.64-71
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• 2007

To investigate the phylogeny of Patellogastropoda, the complete 18S rDNA sequences of nine patellogastropod limpets Cymbula canescens (Gmelin, 1791), Helcion dunkeri (Krauss, 1848), Patella rustica Linnaeus, 1758, Cellana toreuma (Reeve, 1855), Cellana nigrolineata (Reeve, 1854), Nacella magellanica Gmelin, 1791, Nipponacmea concinna (Lischke, 1870), Niveotectura pallida (Gould, 1859), and Lottia dorsuosa Gould, 1859 were determined. These sequences were then analyzed along with the published 18S rDNA sequences of 35 gastropods, one bivalve, and one chiton species. Phylogenetic trees were constructed by maximum parsimony, maximum likelihood, and Bayesian inference. The results of our 18S rDNA sequence analysis strongly support the monophyly of Patellogastropoda and the existence of three subgroups. Of these, two subgroups, the Patelloidea and Acmaeoidea, are closely related, with branching patterns that can be summarized as [(Cymbula + Helcion) + Patella] and [(Nipponacmea + Lottia) + Niveotectura]. The remaining subgroup, Nacelloidea, emerges as basal and paraphyletic, while its genus Cellana is monophyletic. Our analysis also indicates that the Patellogastropoda have a sister relationship with the order Cocculiniformia within the Gastropoda.

• 생명과학회지
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• 제13권4호
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• pp.400-411
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• 2003

5.8S rDNA를 포함한 ITS부위에 대한 염기서열 분석결과, 종에 따라 다양한 염기서열을 가지고 있어 분류에 이용될 수 있었으며, 특히 ITS2부위보다 ITS1부위에서 종에 대한 변이율이 높은 것으로 나타났다. 아울러 균종에 따라 정도의 차이는 있으나 사용된 모든 종들이 서로 계통분류학적 거리가 멀어서 종간의 구분이 명확하게 나타났다. P. tenuipes, I. japonica, P. japonicus는 multiple alignment분석에서 매우 유사한 염기서열을 가지고 있어, 이들 세종은 같은 종이지만 다른 이름으로 불리고 있는 것으로 나타났으며, 아울러 Paecilomyces sp. KACC 40220과 KACC 40656도 동일한 염기서열을 가지고 있어 p. tenuipes로 판단된다. 국내에서 유통되는 동충하초제품 35건과 중국산 1건에 대해 실험한 결과 23건은 P. tenuipes / japonica로, 11건은 C. militaris로, 1건은 B. bassiana로 분류되었으며, 중국산 제품 1건은 C. multiaxialis로 분류되었다.

• Journal of Life Science
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• 제11권2호
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• pp.74-80
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• 2001

The nucleotide sequences of the internal transcribed spacer regions (ITS1 and ITS2) of ribosomal DNA (rDNA), and the 5.85 rRNA gene, have been determined for 13 strains of dinoflagellates in order to analyze the phylo-genetic relationship. The DNA sequences contained considerable variation in the ITS regions, but little in the 5.85 rDNA. In addition, the ITS1 was more variable than the ITS2 in all species examined. The nucleotide length of this region varied from 519 bp to 596 bp depending on the taxa. The investigated taxa were divided into three large groups based on the ITS length, i. e., a group with short ITS region (A. fraterculus and Alexandrium sp.), a with ITS region group (P. micans, P. minimum and P. triestinum) and a with ITS region group (G. impudicum, C. polykrikoides, G. sanguineum, G. catenatum and H. triquetra). The relationship between nucleotide length of ITS1 and that of ITS2 was negative, whereas G+C content and nucleotide length showed positive correlation. In phylogenetic analyses producing NJ trees, the topology was similar cluster and clearly divided the taxa into three groups based on 5.8S rDNA that were similar to those based on morphological characteristics. In particular, G. impudicum was more closely related to G. catenatum than to C. polykrikoides using phylogenetic analysis. From this study, we chew that the length of ITS region contributes to discriminate Korean harmful algal species and ITS analysis is a useful method for resolving the systematic relationships of dinoflagellates.

• Ocean Science Journal
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• 제40권3호
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• pp.155-166
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• 2005

New PCR primers (N=18) were designed for the isolation of complete SSU to LSU rDNA sequences from the dinoflagellate Alexandrium tamarense. Standard PCR, employing each primer set selected for amplifications of less than 1.5 kb, successfully amplified the expected rDNA regions of A. tamarense (Korean isolate, HY970328M). Complete SSU, LSU rDNAs and ITS sequences, including 5.8S rDNA, were recorded at 1,800 bp, 520 bp and 3,393 bp, respectively. The LSU rDNA sequence was the first report in Alexandrium genus. No intron was found in the LSU rRNA coding region. Twelve D-domains within the LSU rDNA were put together into 1,879 bp (44.4% G+C), and cores into 1514 bp (42.8% G+C). The core sequence was significantly different (0.0867 of genetic distance, 91% sequence similarity) in comparison with Prorocentrum micans (GenBank access. no. X16108). The D2 region was the longest in length (300 bp) and highly variable among the 12 D-domains. In a phylogenetic analysis using complete LSU rDNA sequences of a variety of phytoplankton, A. tamarense was clearly separated with high resolution against other species. The result suggests that the sequence may resolve the taxonomic ambiguities of Alexandrium genus, particularly of the tamarensis complex.