• 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.

• 생명과학회지
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• 제23권7호
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• pp.847-853
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• 2013

원추리속 식물은 초본류이며 이 속의 일부 종은 약용으로 중요하다. 이 속의 8개 분류군에 대해 엽록체의 rps16-trnK 부위로 계통관계를 평가하였다. 배당된 서열은 원추리(H. aurantiaca)에서 729 핵산 수로 가장 적었으며 왕원추리(H. fulva var. kwanso)에서 742 핵산 수로 가장 많았다. 그 차이는 염기 삽입에 기인하였다. 비록 일부 인델(indel)과 20개 염기의 삽입이 발견되었지만 서열 내 변이는 염기 치환이 많았다. rps16 - trnK에 의한 한국내 원추리속 분류군들은 높은 지지도로 잘 분리되었다. 애기원추리(H. minor)와 홍도원추리(H. littorea)는 높은 지지도로 같은 분지군을 형성하였으며 이 분지군은 노랑원원추리와 자매군을 형성하였다. 염색체의 수는 기존 보고된 RAPD의 결과와는 일치하지 않으나 본 연구와는 일치하였다.

• 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.

• 한국미생물생명공학회:학술대회논문집
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• 한국미생물생명공학회 2000년도 Proceedings of 2000 KSAM International Symposium and Spring Meeting
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• pp.128-134
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• 2000

In the course of flora analysis of soil Archaea, we found very strange 16S rDNA clones, which could possibly constitute a sister clade from known two archael, Crenarchaeota and Euryarchaeota, lineages. Overall signature sequences showed that the clones were closely related to domains Archaea and Eucarya. However, at least nine nucleotides distinguished the novel clones from domains Archaea and Eucarya. Phylogenetic trees drawn by maximum parsimony, neighbor joining and maximum likelihood methods also showed unique phylogenetic position of the clones. A very specific primer set was synthesized to detect the presence of the novel group of organisms in terrestrial environments. A specific DNA fragment was amplified from all of paddy soil DNAs, and this fact suggests that the novel organisms inhabit paddy soils.

• ALGAE
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• 제27권3호
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• pp.175-187
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• 2012

Hainan is the second largest and southernmost island of China, and it harbors many species of the family Gracilariaceae. In this study, we conducted molecular and morphological analyses of gracilarian specimens collected from Hainan Island, to clarify their taxonomic identity and phylogenetic relationships. Five species of Gracilariaceae in Hainan were determined through maximum likelihood and Bayesian analysis of rbcL sequence data. Based on the phylogenetic trees and morphology, Hainan specimens were identified as three species of Gracilaria, one species of Gracilariopsis, and one species of Hydropuntia, namely, G. salicornia, G. tenuistipitata, Gracilaria sp., Gp. bailiniae and H. edulis. This is the first report of the molecular phylogeny of Gracilariaceae on Hainan Island, and it helps to clarify the taxonomy and distribution of gracilarian species in the Asia-Pacific region.

• BMB Reports
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• 제39권5호
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• pp.522-529
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• 2006

Silk moths are the best studied silk secreting insects and belong to the families Bombycidae and Saturniidae. The phylogenetic relationship between eleven silk producing insects was analyzed using the complete DNA sequence of the internal transcribed spacer DNA 1 locus. The PCR amplification and sequence analysis showed variation in length ranging from 138 bp (Antheraea polyphemus) to 911 bp (Hyalopora cecropia). Microsatellite sequences were found and was be used to distinguish Saturniidae and Bombycidae members. The nucleotide sequences were aligned manually and used for construction of phylogenetic trees based on Maximum parsimony and Maximum likelihood methods. The topology in both the approaches yielded a similar tree that supports the ancestral position of the Antheraea assama.

• Animal Systematics, Evolution and Diversity
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• 제31권4호
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• pp.311-315
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• 2015

Euryalid specimens were collected from Gonghyeonjin and Daejin, Gangwon-do in the East Sea, Korea at a depth of 250-300 m by fishing nets on November 2013 and August 2014. They were identified as Gorgonocephalus arcticus Leach, 1819 belonging to family Gorgonocephalidae of order Euryalida, which was new to the Korean fauna. Nucleotide sequences of partial mitochondrial cytochrome c oxidase I (mt-COI) gene, which was 569 bp in length, were compared among four Gorgonocephalus species, and were subsequently employed to reconstruct phylogenetic trees using the MP, ML, and BI methods. As a result, no sequence difference was found between the G. arcticus mt-COI gene sequences from Korea and Canada, and the two made a strong monophyletic group. With the newly recorded G. arcticus in Korea, in total, four Gorgonocephalus species have been reported in Korea.

• 한국균학회지
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• 제49권2호
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• pp.139-153
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• 2021

The Inocybaceae is a family of ectomycorrhizal fungi belonging to the Agaricales order. Most species in this family produce secondary metabolites, such as muscarine, psilocybin, and other compounds. In the present study, we conducted taxonomic studies on the Inocybaceae based on morphological and molecular phylogenetic analyses for the first time in Korea. As a result, seven species of Inocybaceae were newly recorded: Inocybe caroticolor, I. fuscidula, I. grammatoides, I. latibulosa, I. stellata, Inosperma shawarense, and Mallocybe malenconii. Among them, the genera Inosperma and Mallocybe were described for the first time in Korea. Relevant morphological characteristics, phylogenetic trees, and photographs are provided.

• 식물분류학회지
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• 제51권4호
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• pp.353-362
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• 2021

The chloroplast genome of Glycyrrhiza uralensis Fisch was sequenced to investigate intraspecific variations on the chloroplast genome. Its length is 127,689 bp long (34.3% GC ratio) with atypical structure of chloroplast genome, which is congruent to those of Glycyrrhiza genus. It includes 110 genes (76 protein-coding genes, four rRNAs, and 30 tRNAs). Intronic region of ndhA presented the highest nucleotide diversity based on the six G. uralenesis chloroplast genomes. A total of 150 single nucleotide polymorphisms and 10 insertion and deletion (INDEL) regions were identified from the six G. uralensis chloroplast genomes. Phylogenetic trees show that the six chloroplast genomes of G. uralensis formed the two clades, requiring additional studies to understand it.

• ALGAE
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• 제21권2호
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• pp.175-183
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• 2006

Recent phylogenetic studies of scytosiphonacean brown algae show many conflicts with current classification. In order to clearly define the phylogenetic relationships of the family, we newly sequenced the photosystem I coding psaA gene (1488 base pairs) from 13 taxa (15 samples), of the family, and, for comparison, rbcL from four taxa. The psaA region has more informative sites (17.9%) than the rbcL (13.1%) and the number of nodes supported by over 50% bootstrap values is more in the psaA phylogeny (53 /57 nodes; 93%) than in the rbcL (47/63 nodes; 74.6%). The psaA phylogenies are basically congruent with the rbcL trees, recognizing two major groups in the monophyletic Scytosiphonaceae. The first group included Myelophycus, Petalonia, Scytosiphon, and elongate sack-shaped species of Colpomenia, primarily cold temperate elements with unilocular zoidangia on sporophytes. The second group, although not resolved, consisted of Hydroclathrus, Chnoospora, Rosenvingea, and ball-shaped Colpomenia, primarily warm-temperate taxa with both unilocular and plurilocular zoidangia on sporophytes. Chnoospora is not monophyletic, as was previously shown the paraphyly of Colpomenia, Petalonia, and Scytosiphon. Hydroclathrus clathratus from Korea and Japan was not monophyletic. Our studies show that gametophytic characters are the main source of conflict for the present taxonomy of the family. The psaA region is a useful tool for resolution of phylogenetic relationships within the Scytosiphonaceae.