• Journal of Life Science
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• v.11 no.2
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• pp.83-86
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• 2001

The long terminal repeat (LTR) elements of human endogenous retrovirus (HERV) have been found to be coexpressed with genes located nearby. It has been suggested that the LTR elements have contributed to the genetic variation of human genome connected to various diseases. Recently, HERV-W family was identified in the cerebrospinal fluids and brains of individuals with schizophrenia. Using genomic DNAs derived from schizophrenia, we performed PCR amplification and identified six HERV-W LTR elements. Those LTR elements showed a high degree of sequence similarity (87.7-99.5%) with HERV-W LTR (AF072500). Sequence analysis of the HERV-W LTR elements revealed that clone W-sch1 showed identical sequence with the AC003014 (PAC clone RP1-290B4) derived from human Xq23. Clone W-sch2 was closely related to the AC0072442 derived from human Y chromosome by phylogenetic analysis. Our data suggest that new HERV-W LTR elements in schizophrenia may be very useful for further studies to understand neuropsychiatric diseases.

• Animal cells and systems
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• v.6 no.2
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• pp.167-170
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• 2002

The long terminal repeats (LTRs) of human endogenous retrovirus (HERV) have been found to be coexpressed with sequences of closely located genes. It has been suggested that the LTR elements have contributed to the structural change or genetic variation of human genome connected to various diseases and evolution. We examined the HERV-W LTR elements in various cancer cells (2F7, A43l , A549, HepG2, MIA-PaCa-2, PC-3, RT4, SiHa, U-937, and UO-31). Using genomic DNA from the cancer cells, we performed PCR amplification and identified twelve new HERV-W LTR elements. Those LTR elements showed a high degree of sequence similarity (88-99％) with HERV-W LTR (AF072500). A phylogenetic tree obtained by the neighbor-joining method revealed that HERV-W LTR elements could be mainly divided into two groups through evolutionary divergence. Three HERV-W LTR elements (RT4-2, A43l-1, and UO3l-2) belonged to Group 1, whereas nine LTR elements (2F7-2, A549-1, A549-3, HepG2-3, MP2-2, PC3-1, SiHa-8, SiHa-10, and U937-1) belonged to Group 11. Taken together, our new sequence data of the HERV-W LTR elements may contribute to an understanding of tissue-specific cancer by genomic instability of LTR integration.

• Journal of Life Science
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• v.14 no.4
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• pp.716-725
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• 2004

Sox protein family, a transcription factor, has been found in whole animal kingdom, and contains a sequence-specific DNA binding domain called high mobility group domain (HMG). The Sox protein family based on the amino acid sequence of HMG domain was classified into 10 groups. Each group of Sox family shows significant conservation from nematode to human. The HMG domain affect to various developmental cell differentiation through binding to enhancer and regulating other transcription factors. Recently, many molecular biologists focus their research on the illustration of Sox-related disease, evolution and phylogeny. Especially, stem cell research with Sox gene family is indispensable field for understanding of their biological functions. The understanding of Sox genes may contribute to understand their role in human genetic disease and whole animal evolution.

• Korean Journal of Plant Resources
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• v.27 no.6
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• pp.671-679
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• 2014

Molecular phylogenetic analyses of Korean Elaeagnus L. were conducted using seven species, one variety, one forma and four outgroups to evaluate their relationships and phylogeny. The sequences of internal transcribed spacer regions in nuclear ribosomal DNA were employed to construct phylogenetic relationships using maximum parsimony (MP) and Bayesian analysis. Molecular phylogenetic analysis revealed that Korean Elaeagnus was a polyphyly. E. umbellata var. coreana formed a subclade with E. umbellata. Additionally, the genetic difference between E. submacrophylla and E. macrophylla was very low. Moreover, E. submacrophylla formed a branch from E. macrophylla, indicating that E. submacrophylla can be regarded as a variety. However, several populations of this species were not clustered as a single clade; therefore, further study should be conducted using other molecular markers. Although E. glabra f. oxyphylla was distinct in morphological characters of leaf shape with E. glabra. But E. glabra f. oxyphylla was formed one clade by molecular phylogenetic with E. glabra. Additionally, this study clearly demonstrated that E. pungens occurs in Korea, although it was previously reported near South Korea in Japan and China. According to the results of ITS regions analyses, it showed a resolution and to verify the relationship between interspecies of Korean Elaeagnus.

• Journal of Species Research
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• v.3 no.1
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• pp.7-16
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• 2014

Many species of Lymantria are important forestry pests, including L. dispar which is well known distributed from Asia to North America as an invasive species. Like of most other genera of moths, the systematic of this genus is still in dispute, especially on the monophyly and the relationship within this genus due to the fact that genus is very large and varied. This genus was morphologically defined only by a single aphomorphy. To clarify the monophyly of the genus Lymantria, to reveal the phylogenetic relationship among the Indonesian species, and to establish the genetic characters of Indonesian Lymantria, we analyzed 9 species of Indonesian Lymantria involving 33 other species distributed around the world based on nucleotide sequence variation across a 516-bp region in the CO I gene. The results showed that the base composition of this region was a high A+T biased (C: 0.3333). The results also showed that the monophyly of Lymantria was not supported by bootstrap tests at any tree building methods. Indonesian species was distributed into four different groups but the relationship among them was still in dispute. It indicates that relationships among the basal nodes (groups) proposed here were least valid due to the fact that the number of species may not be enough to represent the real number of species in the nature. Moreover CO I gene sequences alone were not able to resolve their relationships at the basal nodes. More investigations were needed by including more species and other genes that the more conserved.

• ALGAE
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• v.35 no.1
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• pp.1-15
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• 2020

Two strains isolated from a subtropical region in China, were morphologically identified as a Nostoc-like species, but its taxonomic identity was unknown. In this study, these two strains were taxonomically and phylogenetically characterized based on polyphasic approach combining morphological and genetic characteristics. Though both were virtually indistinguishable from Nostoc in field and cultured material, these two strains were phylogenetically distinct from Nostoc based on 16S rRNA phylogeny. The 16S-23S internal transcribed spacer rRNA secondary structure of these strains showed the unique pattern of D1-D1', Box-B, and V3 helix, which distinguished them from other Nostoc-like heterocytous genera. A unique cluster separated from Nostoc sensu stricto supports the establishment of Violetonostoc gen. nov. with the type species as Violetonostoc minutum sp. nov.

• Parasites, Hosts and Diseases
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• v.59 no.1
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• pp.89-95
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• 2021

Microcotyle sebastis is a gill monogenean ectoparasite that causes serious problems in the mariculture of the Korean rockfish, Sebastes schlegelii. In this study, we isolated the parasite from fish farms along the coasts of Tongyeong, South Korea in 2016, and characterized its infection, morphology and molecular phylogeny. The prevalence of M. sebastis infection during the study period ranged from 46.7% to 96.7%, and the mean intensity was 2.3 to 31.4 ind./fish, indicating that the fish was constantly exposed to parasitic infections throughout the year. Morphological observations under light and scanning electron microscopes of the M. sebastis isolates in this study showed the typical characteristics of the anterior prohaptor and posterior opisthaptor of monogenean parasites. In phylogenetic trees reconstructed using the nuclear 28S ribosomal RNA gene and the mitochondrial cytochrome c oxidase I gene (cox1), they consistently clustered together with their congeneric species, and showed the closest phylogenetic relationships to M. caudata and M. kasago in the cox1 tree.

• The Plant Pathology Journal
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• v.37 no.1
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• pp.1-23
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• 2021

Resistance to diseases caused by turnip mosaic virus (TuMV) in crop species of the family Brassicaceae has been studied extensively, especially in members of the genus Brassica. The variation in response observed on resistant and susceptible plants inoculated with different isolates of TuMV is due to a combination of the variation in the plant resistome and the variation in the virus genome. Here, we review the breadth of this variation, both at the level of variation in TuMV sequences, with one eye towards the phylogeny and evolution of the virus, and another eye towards the nature of the various responses observed in susceptible vs. different types of resistance responses. The analyses of the viral genomes allowed comparisons of pathotyped viruses on particular indicator hosts to produce clusters of host types, while the inclusion of phylogeny data and geographic location allowed the formation of the host/geographic cluster groups, the derivation of both of which are presented here. Various studies on resistance determination in particular brassica crops sometimes led to further genetic studies, in many cases to include the mapping of genes, and in some cases to the actual identification of the genes. In addition to summarizing the results from such studies done in brassica crops, as well as in radish and Arabidopsis (the latter as a potential source of candidate genes for brassica and radish), we also summarize work done using nonconventional approaches to obtaining resistance to TuMV.

• Mycobiology
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• v.49 no.6
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• pp.559-581
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• 2021

The coastal marine ecosystems of Vietnam are one of the global biodiversity hotspots, but the biodiversity of marine fungi is not well known. To fill this major gap of knowledge, we assessed the genetic diversity (ITS sequence) of 75 fungal strains isolated from 11 surface coastal marine and deeper waters in Nha Trang Bay and Van Phong Bay using a culture-dependent approach and 5 OTUs (Operational Taxonomic Units) of fungi in three representative sampling sites using next-generation sequencing. The results from both approaches shared similar fungal taxonomy to the most abundant phylum (Ascomycota), genera (Candida and Aspergillus) and species (Candida blankii) but were different at less common taxa. Culturable fungal strains in this study belong to 3 phyla, 5 subdivisions, 7 classes, 12 orders, 17 families, 22 genera and at least 40 species, of which 29 species have been identified and several species are likely novel. Among identified species, 12 and 28 are new records in global and Vietnamese marine areas, respectively. The analysis of enzyme activity and the checklist of trophic mode and guild assignment provided valuable additional biological information and suggested the ecological function of planktonic fungi in the marine food web. This is the largest dataset of marine fungal biodiversity on morphology, phylogeny and enzyme activity in the tropical coastal ecosystems of Vietnam and Southeast Asia. Biogeographic aspects, ecological factors and human impact may structure mycoplankton communities in such aquatic habitats.

• Korean Journal of Plant Resources
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• v.25 no.6
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• pp.762-772
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• 2012

The objective of this study was to analyze the genetic diversity using SSR marker and investigate the fatty acid composition of perilla (P. frutescens var. frutescens) germplasm. Genetic diversity among 95 accessions, which consisted of 29 weedy types and 66 landrace accessions, was evaluated based on 12 SSR markers carrying 91 alleles. The mean values of observed ($H_O$) and expected heterozygosities ($H_E$) were 0.574 and 0.640, respectively, indicating a considerable amount of polymorphism within this collection. A genetic distance-based phylogeny grouped into two distinct groups, which were the landrace, moderate and weedy type, genetic distance (GD) value was 0.609. The physicochemical traits about crude oil contents and fatty acid compositions were analyzed using GC. Among tested germplasm, the total average oil contents (%) showed a range from 28.57 to 49.67 %. Five fatty acids and their contents in the crude oils are as follows: ${\alpha}$-linolenic acid (41.12%-51.81%), linoleic acid (15.38%-16.43%), oleic acid (18.93%-27.28%), stearic acid (2.56%-4.01%), and palmitic acid (7.38%-10.77%). The average oil content of wild types was lower than landrace, and the oil content of middle genotype accessions was higher than other germplasm, but no significant variation between landrace and wild types was shown. Nevertheless, IT117174, landrace of Korea, was highest in crude oil content (47.11%) and linolenic acid composition (64.58%) among the used germplasm. These traits of the selected accessions will be helped for new functional plant breeding in perilla crop.