• Journal of Microbiology
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• 제45권6호
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• pp.521-527
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• 2007

Several yeast strains degrading malic acid as a sole carbon and energy source were isolated from Korean wine pomace after enrichment culture in the presence of malic acid. Among them, the strain designated as KMBL 5774 showed the highest malic acid degrading ability. It was identified as Issatchenkia orientalis based on its morphological and physiological characteristics as well as the nucleotide sequences of the internal transcribed spacer (ITS) 1-5.8S rDNA-ITS II region. Phylogenetic analysis of the ITS I-5.8S rDNA-ITS II sequences showed that the KMBL 5774 is the closest to I. orientalis zhuan 192. Identity of the sequences of the KMBL 5774 was 99.5% with those of I. orientalis zhuan 192. The optimal pH of the media for the growth and malic acid degradation by the yeast was between 2.0 and 3.0, suggesting that the strain is an acidophile. Under the optimized conditions, the yeast could degrade 95.5% of the malic acid after 24 h of incubation at $30^{\circ}C$ in YNB media containing 2% malic acid as a sole carbon and energy source.

• 생명과학회지
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• 제27권1호
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• pp.89-94
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• 2017

포도과(Vitaceae) 포도속(Vitis) 식물들 19종의 intergenic spacer 1 및 intergenic spacer 2의 염기서열을 Genbank에서 수집하였다. 그러나 국내에서 흔하게 발견되는 포도과 포도속 식물인 까마귀머루(Vitis thunbergii var. sinuata)와 포도과 개머루속 식물인 개머루(Ampelopsis brevipedunculata var. heterophylla)의 염기서열은 Genbank에서 발견할 수 없었다. 따라서 개머루와 까마귀머루를 채집하고 genomic DNA를 분리하여서 18S rDNA, ITS1, 5.8S rDNA, ITS2 및 28S rDNA의 일부를 증폭하고, 그 염기서열을 분석하였다. 이렇게 얻어진 염기서열을 다른 포도속 식물들의 염기서열과 MUSCLE (Multiple sequence comparison by log-expectation) algorithm으로 서로 비교하여 neighbor-joining tree 및 pairwise distance (p-distance)를 계산해 보았다. 그 결과 국내 자생종인 개머루와 까마귀 머루는 서로 간에는 높은 상동성을 보이지만 외국의 포도속 식물들과는 유전적 상관관계가 상당히 멀다는 것을 발견할 수 있었다. 이것은 아마도 우리나라 자생종들의 경우에 오랜 시간 동안 외국의 포도속 식물들과 지리적으로 격리된 상태에서 독립적으로 진화한 결과가 아닌가 생각된다. 또한 개머루와 까마귀머루의 염기서열의 상동성이 높은 데에도 불구하고, 형태를 기준으로 하는 기존의 분류체계에 따라서 개머루는 개머루속으로 까마귀머루는 포도속으로 분류가 되고 있다. 형태를 기준으로 하는 기존의 분류체계와 염기서열을 기준으로 하는 유전적 분류체계간의 괴리를 본 연구에서 다시 한 번 확인할 수 있었다.

• 생명과학회지
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• 제25권2호
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• pp.243-248
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• 2015

국내에 자생 중인 도깨비엉겅퀴(Cirsium shantarense), 물엉겅퀴(Cirsium nipponicum), 정영엉겅퀴(Cirsium chanroenicum) 각 1개체 및 엉겅퀴(Cirsium japonicum) 8개체를 전국의 여러 지점에서 채집하였다. 채집된 식물들의 genomic DNA를 분리하여서 18S rDNA, ITS1, 5.8S rDNA, ITS2 및 28S rDNA의 일부를 증폭하고, 그 염기서열 및 Genbank에 등록되어 있는 다른 Cirsium 속 식물들의 염기서열을 분자유전학적으로 비교하여 유연관계를 분석하였다. 그 결과 고려엉겅퀴, 정영엉겅퀴, 물엉겅퀴, 큰엉겅퀴 및 엉겅퀴 종의 식물들은 모두 뚜렷이 독립된 그룹을 형성하고 있는 것을 알 수 있었다. 그러나 도깨비엉겅퀴는 비록 두화가 아래를 향하고 있지만 두화가 위를 향하는 엉겅퀴들과 ITS 염기서열은 유사하였다. 또한 정영엉겅퀴와 고려엉겅퀴는 형태학적으로는 구분이 거의 불가능하지만 ITS 염기서열에 기초한 분자유전학적 분석으로는 뚜렷이 다른 그룹임을 확인하였다. 채취된 엉겅퀴 및 도깨비엉겅퀴의 silymarin 생산 여부를 분석해 본 결과, silymarin이 공통적으로 존재하는 것으로 나타났다. 따라서 silymarin 생합성 능력은 Cirsium 속 식물들에서 공통적인 특징임을 알 수 있었다.

• Journal of Microbiology and Biotechnology
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• 제14권4호
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• pp.816-821
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• 2004

A reliable molecular phylogenetic method to identify Hericium erinaceum, the most industrially valuable species in the Hericium genus, was established. Sequencing and phylogenetic analyses of the PCR-amplified ITS and 5.8S rDNA from Hericium fungi, including 6 species and 23 isolates, showed that variation in nucleotide sequences and size exists in both ITS1 and ITS2 regions, but not in the 5.8S region. These two ITS regions provided different levels of information on the relationship of H. erinaceum to other Hericium species. Based on the ITS1 sequence, both the parsimony and neighbor joining trees clearly distinguished Asian H. erinaceum isolates from other Hericium species and isolates. The intraspecific divergence of the ITS2 region was suitable to dissect the Asian H. erinaceum isolates into a few groups.

• Journal of Species Research
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• 제12권4호
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• pp.307-312
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• 2023

Oxytricha multilineata, Mixophrya pantanalensis pantanalensis, and Caudiurostyla sinensis were isolated from soil samples collected from Cheongju-si and Yeoju-si, confirmed as new to South Korea. Oxytricha multilineata was distinguished from other congeners by seven dorsal kineties and dorsal bristles about 15 ㎛ long. Mixophrya pantanalensis pantanalensis was characterized by five to seven lithosomes and six dorsal kineties. Caudiurostyla sinensis was characterized by colorless cortical granules present, 10-14 midventral pairs, 7-9 left and 6-9 right marginal rows and four or five dorsal kineties. We determined the ribosomal DNA sequences (including 18S rDNA, ITS1, 5.8S rDNA, ITS2, and partial 28S rDNA) from above three species. And the genetic distances were compared with their congeners.

• Animal Systematics, Evolution and Diversity
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• 제35권4호
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• pp.186-190
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• 2019

DNA barcoding of two marine tintinnids, Eutintinnus rectus and Schmidingerella arcuata, was performed using four samples collected from different sites in the north-eastern coast of South Korea. The loricae morphology was observed by light and scanning electron microscopy. Molecular data were analyzed using five nuclear ribosomal DNA markers(18S, ITS1, 5.8S, ITS2, and 28S genes) and one mitochondrial marker (CO1 gene). The intraspecific pairwise differences of E. rectus and S. arcuata in the CO1 gene were 0.0-0.2% and 0.0-0.6%, respectively, while there were no differences in the 18S rDNA sequences.

• Journal of Life Science
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• 제11권2호
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• pp.126-134
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• 2001

The phylogenetic tree displayed the presence of five groups in the Phellinus genus, which were distinguished based on their morphology. Most of the p. linteus appeared a cluster which was highly significant with the exception of P. linteus KACC 500122 and KACC 500411. They formed the sister taxa of P 1inteus where P. baumii, Phellinus sp. MPNU 7003, MPNU 7007, and MPNU 7010 had similar morphological characteristics. Also, P. nigricans IMSNU 32024 and P. pini var, carniformans IMSNU 32031 were grouped in the same cluster with P. igniarius KCTC 6227, KCTC 6228, and P. chrysoloma KCTC 6225 extracted from the Gen-Bank database. P. torulosus IMSNU 32028 and Phellinus sp. MPNU 7011 formed a closed group, however, these species had a distant taxa when compared with the other Phellinus species. The nucleotide sequences of the internal transcribed spacer (ITS) regions of ribosomal DNA (rDNA) including the 5.85 rDNA were determined from 24 strains of the Phellinus genus in order to analyze their phylogenetic relationship. These fungi were divided into two basic groups based on their ITS length, however, this grouping was different from that based on their morphological characteristics. Although various ITS sequences were ambiguously aligned, conserved sites were also identified. Accordingly, a neighbor-joining tree was constructed using the nucleotide sequence data of the conserved sites of the ITS regions and the 5.8S rDNA.

• Molecules and Cells
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• 제25권4호
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• pp.510-522
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• 2008

To construct the molecular systematics of the genus Megoura (Hemiptera: Aphididae), DNA based-identification was performed using four mitochondrial and three nuclear DNA regions: partial cytochrome c oxidase I (COI), partial tRNA-leucine + cytochrome c oxidase II (tRNA/COII), cytochrome b (CytB), partial 12S rRNA + tRNA-valine + 16S rRNA (12S/16S), elongation factor-1 alpha ($EF1{\alpha}$), and the internal transcribed spacers 1 and 2 (ITS1, ITS2). Pairwise sequence divergences between taxa were compared, and phylogenetic analyses were performed based on each DNA region separately, and the combined datasets. COI, CytB, $EF1{\alpha}$, ITS1, and ITS2 were relatively effective in determining species and resolving their relationships. By contrast, the sequences of tRNA/COII and 12S/16S were not able to separate the closely related species. CytB and $EF1{\alpha}$ gave better resolution with higher average sequence divergences (4.7% for CytB, 5.2% for $EF1{\alpha}$). The sequence divergence of COI (3.0%) was moderate, and those of the two ITS regions (1.8% for ITS1, 2.0% for ITS2) were very low. Phylogenetic trees were constructed by minimum evolution, maximum parsimony, maximum likelihood, and Bayesian phylogenetic analyses. The results indicated that the phylogenetic relationships between Megoura species were associated with their host preferences. Megoura brevipilosa and M. lespedezae living on Lespedeza were closely related, and M. nigra, monophagous on Vicia venosa, was rather different from M. crassicauda, M. litoralis, and M. viciae, which are oligophagous on Lathyrus and Vicia. The three populations of M. crassicauda formed a clade separated from M. litoralis and M. viciae. Nevertheless M. litoralis and M. viciae, which are morphologically similar, were not separated due to negligible sequence divergence. We discuss the phylogenetic relationships of the Megoura, and the usefulness of the seven DNA regions for determining the species level phylogeny of aphids.

• Mycobiology
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• 제38권2호
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• pp.89-96
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• 2010

This study evaluated the optimal vegetative growth conditions and molecular phylogenetic relationships of eleven strains of Agrocybe cylindracea collected from different ecological regions of Korea, China and Taiwan. The optimal temperature and pH for mycelial growth were observed at $25^{\circ}C$ and 6. Potato dextrose agar and Hennerberg were the favorable media for vegetative growth, whereas glucose tryptone was unfavorable. Dextrin, maltose, and fructose were the most effective carbon sources. The most suitable nitrogen sources were arginine and glycine, whereas methionine, alanine, histidine, and urea were least effective for the mycelial propagation of A. cylindracea. The internal transcribed spacer (ITS) regions of rDNA were amplified using PCR. The sequence of ITS2 was more variable than that of ITS1, while the 5.8S sequences were identical. The reciprocal homologies of the ITS sequences ranged from 98 to 100%. The strains were also analyzed by random amplification of polymorphic DNA (RAPD) using 20 arbitrary primers. Fifteen primers efficiently amplified the genomic DNA. The average number of polymorphic bands observed per primer was 3.8. The numbers of amplified bands varied based on the primers and strains, with polymorphic fragments ranging from 0.1 to 2.9 kb. The results of RAPD analysis were similar to the ITS region sequences. The results revealed that RAPD and ITS techniques were well suited for detecting the genetic diversity of all A. cylindracea strains tested.

• 한국해양바이오학회지
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• 제2권1호
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• pp.60-67
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• 2007

For the first time in Vietnam, morphological and molecular studies of a species belonging to Bacillariophyceae collected in Northern coast of Vietnam are presented. Observations with microscope showed that this species belong to genus: Pseudo-nitzschia and seem like P. pungens. Sequence data from the partial 18S small subunit ribosomal RNA gene (18S rDNA) and the internal transcribed spacer 1 - 5.8S - internal transcribed 2 have been used to determine clearly and generate a phylogenetic framework of the obtained sequences to previously reported sequences in GenBank. These results allowed us to highlight described species of Bacillariophyceae in Northern coast of Vietnam. Furthermore, accumulation of molecular study would be helpful for the identification of scientific name of harmful algal species and further taxonomic studies in Vietnam.