• ALGAE
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• v.21 no.3
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• pp.283-286
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• 2006

This study carried out phylogenetic analysis of dinoflagellate Gonyaulax polygramma which was responsible for a harmful algal bloom episode in Korea in 2004. Molecular phylogenetic tree inferred from the partial LSU rDNA data showed that G. polygramma came up among the monophyletic Gonyaulax clade, but did not have apparent genetic affiliation to other Gonyaulax species. This result appears to be consistent with characteristic morphological features of G. polygramma such as epitheca sharply tapering to the apex and thecal plates ornamented with numerous longitudinal striations.

• Journal of Microbiology
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• v.41 no.3
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• pp.232-238
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• 2003

Previous phylogenetic studies on human immunodeficiency virus type 1 (HIV-1) isolated from Korean patients suggest that the major subtype of Korean isolate is subtype B. In this subtype, some of the Korean isolates seem to be clustered exclusively of foreign isolates. Presence of this so-called “Korean clade” among Korean isolates is unique but needs verification since the number of Korean isolates used in previous studies was limited. This study aimed to identify the presence of the “Korean clade” by molecular phylogenetic analysis using all the Korean nef gene sequences registered in the NCBI GenBank (N=243) together with 32 reference strains and 77 foreign isolates. Extensive analysis of the nef gene nucleotide sequences by neighbor-joining method revealed the following. Most (83.1 ％) of the Korean isolates belonged to subtype B, and 81.2％ of subtype B were clustered together and excluded foreign isolates (bootstrap value=91.9％ ). Within Korean subtype B cluster, no characteristic subcluster formation was evident since the bootstrap values for the subcluster were very low. Due to limited information, the phylogenetic analysis failed to identify the epidemiological linkage among specific groups such as homosexuals and hemophiliacs within the Korean subtype B cluster. Detailed analysis and epidemiological information are needed to clarify the origin and significance of the Korean subtype B cluster.

• Journal of Microbiology and Biotechnology
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• v.10 no.6
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• pp.823-828
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• 2000

The complete nucleotide sequence of hepatitis B virus DNA isolated from Korean patient serum was determined and characterized, and its phylogenetic relation was then investigated. The viral genome was 3,215 base pairs long and included four well known open reading frames (i.e. surface antigens, core antigens, X protein and DNA polymerase). The sequence of the surface antigen showed that the HBV genome under investigation, designated HBV 315, was characteristic of subtype adr. A phylogenetic analysis using the total genome sequence revealed that HBV315 was grouped into genomic group C together with isolates from Japan, China, Thailand, Polynesia, and New Caledonia. The mean percent similarity between HBV315 and other HBV isolates in genomic group C was 97.25%, and that with other genomic groups ranged from 86.16% to 91.25%. The predicted amino acid sequences of HBV315 were compared with two closely related subtype adr isolates, M38636 and D12980. The results showed that the X gene product was identical in the three strains, while there were significant amino acid sequence differences between HBV315 and M38636 in the Pre-S1 and Pre-S2 regions.

• Korean Journal of Plant Taxonomy
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• v.50 no.4
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• pp.385-394
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• 2020

To elucidate the molecular phylogeny of Neottia japonica, which is a terrestrial orchid distributed in East Asia, the internal transcribed spacer (ITS) of nuclear DNA and the matK of chloroplast DNA were used. A total 22 species of 69 accessions for ITS and 21 species of 114 accessions for matK phylogeny were analyzed with the maximum parsimony and Bayesian methods. In addition, we sought to establish a correlation between the distribution, morphology of the auricles and genetic association of N. japonica with phylogenetic data. The phylogenetic results suggest that N. japonica is monophyletic and a sister to N. suzukii in terms of the ITS phylogeny, while it is paraphyletic with N. suzukii in terms of the matK phylogeny. N. japonica and N. suzukii show similar morphologies of the lip and column, they both flower in April, and they are both distributed sympatrically in Taiwan. Therefore, it appears to be clear that N. japonica and N. suzukii are close taxa within Neottia, although there is incongruence between the nrDNA and cpDNA phylogenies of N. japonica. The incongruence between the two datasets may have various causes, meaning that further studies are needed to confirm the evolutionary process of N. japonica. The phylogenetic status of N. kiusiana, which was not included in previous studies, was as a sister to N. nidus-avis. Meanwhile, the ITS and matK phylogenies are unsuitable for identifying genetic associations with the characteristic of auricles. The phylogenetic topologies of Korean, Taiwanese and mainland Chinese individuals suggest that the populations of N. japonica in Korea originated from China's mainland and island areas. The characterization of regional gene differences could provide useful preliminary data for future studies.

• The Korean Journal of Mycology
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• v.47 no.3
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• pp.181-186
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• 2019

A designated fungal isolate, KNU-US-1802E was isolated from the soil in Uiseong, Korea. To identify characteristics of the isolate, it was cultured on PDA media for 6 days at $35^{\circ}C$. Colonies on PDA are flat, light gray, dense, with entire margins; reverse dark gray to black, with white margins. Aerial mycelia were smooth-walled, hyaline and 40~42 mm diameter after 6 days at $35^{\circ}C$. Conidia were hyaline, one-celled, ellipsoidal to fusiform, forming long chains with average length ${\times}$ width of $5.0{\pm}0.3{\times}2.9{\pm}0.2{\mu}m$. Molecular analysis indicates that the internal transcribed spacer (ITS) region and partial beta-tubulin (tub2) gene sequence showed 100% and 99% similarities, respectively with Acrophialophora ellipsoidea CGMCC 3.15255 collected from China. Phylogenetic analysis by the neighbor-joining (NJ) method shows that the KNU-US-1802E was clustered with A. ellipsoidea CGMCC 3.15255 in a phylogenetic tree constructed using the concatenated sequences of ITS region and tub2 gene sequences with a high bootstrap value. Based on these findings, the isolate KNU-US-1802E was identified as Acrophialophora ellipsoidea, and this is the first report of this isolate in Korea.

• Journal of Ecology and Environment
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• v.41 no.1
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• pp.9-18
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• 2017

Background: Species in the heterokont genus Synura are colonial and have silica scales whose ultrastructural characteristics are used for classification. We examined the ultrastructure of silica scales and molecular data (nuclear SSU rDNA and LSU rDNA, and plastid rbcL sequences) to better understand the taxonomy and phylogeny within the section Petersenianae of genus Synura. In addition, we report the first finding of newly recorded Synura species from Korea. Results: We identified all species by examination of scale ultrastructure using scanning and transmission electron microscopy (SEM and TEM). Three newly recorded species from Korea, Synura americana, Synura conopea, and Synura truttae were described based on morphological characters, such as cell size, scale shape, scale size, keel shape, number of struts, distance between struts, degree of interconnections between struts, size of base plate pores, keel pores, base plate hole, and posterior rim. The scales of the newly recorded species, which belong to the section Petersenianae, have a well-developed keel and a characteristic number of struts on the base plate. We performed molecular phylogenetic analyses based on sequence data from three genes in 32 strains (including three outgroup species). The results provided strong statistical support that the section Petersenianae was monophyletic, and that all taxa within this section had well-developed keels and a defined number of struts on the base plate. Conclusions: The phylogenetic tree based on sequence data of three genes was congruent with the data on scale ultrastructure. The resulting phylogenetic tree strongly supported the existence of the section Petersenianae. In addition, we propose newly recorded Synura species from Korea based on phylogenetic analyses and morphological characters: S. americana, S. conopea, and S. truttae.

• KSBB Journal
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• v.19 no.1
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• pp.42-49
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• 2004

A gene coding for epoxide hydrolase (EH) of Aspergillus niger LK, a fungus possessing the enantioselective hydrolysis activity for racemic epoxides, was characterized by phylogenetic analysis. The deduced protein of A. niger LK epoxide hydrolase shares significant sequence similarity with several bacterial EHs and mammalian microsomal EHs (mEH) and belongs to the a/${\beta}$ hydrolase fold family. EH from A. niger LK had 90.6% identity with 3D crystal structure of lqo7 in Protein Data Bank. Sequence comparison with other source EHs suggested that Asp$\^$l92/, Asp$\^$374/ and His$\^$374/ constituted the catalytic triad. Based on the multiple sequence comparison of the functional and structural domain sequence, the phylogenetic tree between relevant epoxide hydrolases from various species were reconstructed by using Neighbor-Joining method. Genetic distances were so far as 1.841-2.682 but characteristic oxyanion hole and catalytic triad were highly conserved, which means they have diverged from a common ancestor.

• Journal of the korean society of oceanography
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• v.39 no.3
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• pp.163-171
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• 2004

Sequences of the large subunit ribosomal (LSD) rDNA D1-D2 region of Alexandrium catenella(=A. sp. cf. catenella) and A. tamarense isolates, which were collected along the Korea coasts, were analyzed to understand their phylogenetic relationships and geographical distributions. All A. catenella and A. tamarense isolates belonged to the A. tamarense/catenella/fundyense complex and were grouped with the North American and temperate Asian ribotypes, respectively, regardless of the presence or absence of a ventral pore in the first apical plate. A consistent and peculiar characteristic that differentiated the Alexandrium isolates was amplification of a second PCR product with a lower molecular weight in addition to the predicted one; ten A. catenella isolates belonging to the temperate Asian ribotype yielded this additional PCR product. Sequence alignment revealed that the shorter PCR product resulted from an unusual large deletion of 87 bp in the LSD rDNA D1 domain. The North American and temperate Asian ribotypes were prevalent along the Korean coasts without geographical separation. Given the high genetic homogeneity among widely distributed Alexandrium populations, each ribotype appeared to be pandemic rather than to constitute a distinct regional population.

• 보존과학연구
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• s.25
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• pp.47-74
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• 2004

We investigated the nucleotide substitution and insertion polymorphism of the hypervariable region Ⅰ and Ⅱ in mt DNA by sequencing ancient DNA from 51 ancient bones and teeth excavated at Nuk-do and Yimdang-dong in Korea. It revealed 35 sequence types from the ancient Korean. Of these, different sequences were 34 sequences. There were 19 and 38 base substitutions in HVI and HVⅡ, respectively. Some substitutions were characteristic of East Asian populations as compared with data reported on Caucacianpopulations,16051, 16150, 16172, 16223 in region I and 73, 263 in region II were noted as polymorphic sites, respectively. These were distributed evenly along the control region, though the frequency of each site was variable. Nucleotide substitution rather than insertion and deletion was the prevalent pattern of variation. Insertion of cytosine between312 and 315 in region HVⅡ were detected up to 98% in 51 ancient bone samples. This sequence data represents a phylogenetic tree using NTI DNA Suite computer program. The phylogenetic tree showed that mt DNA sequences of Nuk-do bones were relative to west Siberian and Indonesian. The usefulness of mt DNA sequencing in ancient Korean population excavated atarchaeological sites is based on biological and historical evidence for origin and migration of ancient Korean.

• Korean Journal of Veterinary Research
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• v.48 no.2
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• pp.153-159
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• 2008

Newcastle disease virus (NDV) is the causative agent of a highly contagious and devastating Newcastle disease of poultry. A NDV (isolate DK1/07) was isolated from apparently healthy wild spot-billed ducks (Anas poecilorhyncha) captured at upper branch of the SapGyo Creek in Chungbuk province, Korea during early 2007. The DK1/07 isolate of minimum chicken embryo lethal dose killed all SPF chicken embryos within 60 h. The cleavage site of the F protein possessed the amino acid sequence $^{112}R-R-Q-K-R-F^{117}$, which is a motif characteristic of virulent NDV strains. The F protein-based phylogenetic analysis revealed that the DK1/07 duck isolate was included in the cluster of genotype VIId and most closely related to recent NDV isolates obtained from chicken farms in Korea. Epidemiological importance of virulent NDV from wild duck is discussed.