• Korean Journal of Plant Resources
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• v.32 no.6
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• pp.644-668
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• 2019

Dysphania ambrosioides (L.) Mosyakin & Clemants which belongs to Chenopodiaceae/Amaranthaceae sensu in APG system has been known as a useful plant in various fields as well as an invasive species spreading all over the world. To understand its phylogenetic relationship with neighbour species, we completed chloroplast genome of D. ambrosioides collected in Korea. Its length is 151,689 bp consisting of four sub-regions: 83,421 bp of large single copy (LSC) and 18,062 bp of small single copy (SSC) regions are separated by 25,103 bp of inverted repeat (IR) regions. 128 genes (84 protein-coding genes, eight rRNAs, and 36 tRNAs) were annotated. The overall GC content of the chloroplast genome is 36.9% and those in the LSC, SSC and IR regions are 34.9%, 30.3%, and 42.7%, respectively. Distribution of simple sequence repeats are similar to those of the other two Dysphania chloroplasts; however, different features can be utilized for population genetics. Nucleotide diversity of Dysphania chloroplast genomes 18 genes including two ribosomal RNAs contains high nucleotide diversity peaks, which may be genus or species-specific manner. Phylogenetic tree presents that D. ambrosioides occupied a basal position in genus Dysphania and phylogenetic relation of tribe level is presented clearly with complete chloroplast genomes.

• Journal of Veterinary Clinics
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• v.23 no.4
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• pp.405-410
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• 2006

Using internal transcribed spacer 1 (ITS1) region ribosomal DNA sequences from 9 strains of Microsporum canis and 5 strains of Microsporum gypseum isolated from dogs and a cat with dermatophytosis, we demonstrated the mutual phylogenetic relationship of these strains. Nucleotide sequence analysis of the ITS 1 gene fragments from the 9 strains of M canis had the 100% nucleotide sequence similarities and the 5 strains of M gypseum also had the 100% nucleotide sequence similarities. The phylogenetic analysis of the nucleotide sequences of the 9 strains of M canis formed a nested cluster with the reference strains of M canis originating from USA, Australia, Japan, and Europe. M canis were genetically distinct from the other reference strains of Microsporum spp, but M distortum, M equinum, and M. ferrugineum were genetically very close to M canis. M gypseum from a cluster in the phylogenetic tree with M canis as an outgroup. The molecular analysis of ITS 1 genes provided the useful information for the identification of these microsporum species and the understanding of their relationship.

• Korean Journal of Veterinary Research
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• v.43 no.2
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• pp.219-230
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• 2003

Porcine epidemic diarrhea virus(PED), a member of Coronaviridea, is the etiological agent of enteropathogenic diarrhea in swine. The purpose of this study was to investigate genetic characteristic of PEDV isolated in Korea. Nucleocapsid(N) gene and membrane (M) gene of recent Korean PEDV strains isolated in 2001 were amplified, cloned, sequenced and analyzed. N gene of seven Korean PEDV field isolates bad 94.5% to 99.4% nucleotide and 92.4% to 99.4% amino acid sequence homology each other. Nucleotide and amino acid sequences of Korean field PEDVs were different from published foreign PEDVs, showing 95.1% to 98.0% nucleotide and 93.5% to 97.6% amino acid sequence homology. By phylogenetic tree analysis on based nucleotide sequences, PEDVs were clustered into four groups. By phylogenetic tree analysis based on amino acid sequences. PEDVs were clustered into five groups. M gene of our Korean PEDV field isolates had 99.6% to 100% nucleotide and 98.7% to 100% amino acid sequence homology each other. Nuclotide and amino acid sequences of Korean field PEDVs were different from published foreign PEDVs, showing 98.5% to 98.8% nucleotide and 97.3% to 97.8% amino acid sequence homology. By phylogenetic tree analysis based on nucleotide and amino acid sequences, PEDVs were clustered into two groups which were Korean PEDV isolate group and foreign PEDV isolate group.

• Korean Journal of Veterinary Service
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• v.36 no.1
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• pp.23-30
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• 2013

An avian rotavirus (AvRV-2) was isolated from feces of broilers suffering from acute gastroenteritis in 2011. It was the first avian rotavirus isolated in Korea. To investigate the molecular characteristics of AvRV-2, the VP4, VP6, VP7 and NSP4 gene nucleotide sequences were determined and compared with those of rotavirus strains available in the GenBank database. The phylogenetic tree of VP7 gene showed that AvRV-2 had a high degree of nucleotide sequence homology (93.4% to 94.7%) with those of rotaviruses belonging to genotype G19 cluster. The phylogenetic tree of the VP4 gene revealed a high degree of nucleotide sequence homology (95.8% to 95.9%) with genotype P[30] rotaviruses isolated from chickens. The VP6 and NSP4 gene nucleotide sequences showed the highest identities with those of avian strains with 95.3% to 96.4% and 90.3% to 92.2%, respectively. Genetic characterization of the VP4, VP6, VP7 and NSP4 showed that AvRV-2 strain was most closely related to chicken rotavirus strains from Germany and Japan. Comparative nucleotide sequences and phylogenetic analysis indicated that avian rotavirus isolated from broilers belonged to genotype G19P[30] and it was the first report on avian rotavirus infection in Korea.

• The Journal of Korean Society of Virology
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• v.26 no.2
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• pp.251-258
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• 1996

The V3 loop, a hypervariable domain of envelope glycoprotein, has an essential role in viral infectivity and has a major epitope for type-specific neutralizing antibody. In order to investigate genetic diversity of V3 region of gp120 of human immunodeficiency virus type 1 (HIV-1) isolated from Korean patients, DNA sequences encoding the C2 to V3 region were amplified by nested polymerase chain reaction (PCR) from uncultured peripheral blood mononuclear cells obtained from 15 HIV-1 seropositive patients and nucleotide sequences were determined. All nucleotide sequences from fifteen patients were compared with 8 distinctive subtypes (A-H) and another subtype O. Phylogenetic analysis was carried out with PHYLIP ver 3.5 (Dnapars) program. Of the 15 isolates, 14 HIV-1 subjects were clustered with subtype B, while one was clustered with subtype C. Intra-subtype B distance at the nucleotide and deduced amino acid level were maximum 17.7% and 37.0%, respectively. Intra-patient distance at the nucleotide and deduced amino acid level were maximum 7.3% and 17.8%, respectively. Analysis of the nucleotide sequences revealed that Korean types have relatively well conserved sequences. These findings could be useful for assessing the source of infection and developing an AIDS vaccine.

• International Journal of Industrial Entomology and Biomaterials
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• v.37 no.2
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• pp.82-89
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• 2018

This study was carried out to understand phylogenetic relationships of the 30 mulberry cultivars converved in Korea based on the ITS rDNA region, and they were compared to 40 reference sequences from GenBank. The size and the G+C content of the ITS rDNA gene regions from the 30 Korean mulberry cultivars and 40 reference sequences varied from 612-630 bp and 58.19-61.62%, respectively. Based on the results of the comparative phylogenetic analysis of the ITS rDNA regions of the 30 Korean mulberry cultivars and 40 reference sequences, they were divided into three groups (Group 1, 2, and 3) and two subgroups (Group 1A and 1B within Group 1). The sequence lengths of the Korean mulberry cultivar numbers 1-26 and 27-30 were 615 bp and 616 bp, respectively. At 205 bp location of ITS1 rDNA region, the cultivar numbers 1-26 contain the nucleotide thymine but the cultivar numbers 27-30 contain the nucleotide adenine. In addition, the insertion of the nucleotide adenine at 206 bp location was found only in the four Korean mulberry cultivars (numbers 27-30). Based on these sequence information and phylogenetic result, the 30 Korean mulberry cultivars were identified as M. alba and M. australis. This study will contribute to the construction of genetic database constructions and accurate variety identifications for unidentified mulberry varieties in Korea.

• Fisheries and Aquatic Sciences
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• v.13 no.4
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• pp.272-277
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• 2010

Seagrasses are marine angiosperms of ecological importance in providing shelter and food to aquatic species as well as maintaining the carbon cycle on earth. Phyllospadix iwatensis is a seagrass of the family Zosteraceae and is distributed along the eastern coast of Korea. The nucleotide sequences of P. iwatensis nuclear genes encoding 18S ribosomal RNA (rRNA) and internal transcribed spacer-1 (ITS-1) were determined for molecular phylogenetic analysis. Genomic DNA was isolated from P. iwatensis and used for PCR amplification of 18S rRNA and ITS-1. Examination of the 18S rRNA sequence of P. iwatensis showed a close (99% similarity) relationship to Zostera noltii, another genus of Zosteraceae, but a distant (84% similarity) evolutionary relationship to other macroalgal Laminariales species. Further discrepancies found in ITS-1 nucleotide sequences between closely related species indicate that the sequence information could be used for species identification.

• Journal of Life Science
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• v.11 no.2
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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.

• Journal of fish pathology
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• v.22 no.3
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• pp.211-218
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• 2009

In this study, we have compared the genome of marine birnavirus (MABV) detected from starry flounder Platichthys stellatus and olive flounder Paralichthys olivaceus. A molecular analysis based on the nucleotide sequence (433 bases) of VP2-NS-VP3 region revealed that MABV (08-KU) from starry flounder showed 98% similarity with MABV Y6 isolated from Yellowtail Seriola quinqueradita in Japan (Accession no: AY283781) and with other aquabirnaviruses identify more than 76%. Comparison with MABV strains (06-KP, 08-KC) from olive flounder and MABV Y6 strain showed 97-98% sequence identities. Phylogenetic analysis was performed in order to examine the relationship among previously determined aquatic birnaviruses isolates showed that MABV and IPNV strains were classified into seven clusters. Three isolates from starry flounder and olive flounder in this study, belong to the genogroup VII including MABV Y6 strain and other aquabirnaviruses isolated from marine fish and molluscan shellfish in Japan. This report is the first description of a MABV from starry flounder in Korea.

• Korean Journal of Plant Taxonomy
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• v.51 no.4
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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.