• Parasites, Hosts and Diseases
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• v.54 no.2
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• pp.173-179
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• 2016

Echinostoma hortense (Digenea: Echinostomatidae) is one of the intestinal flukes with medical importance in humans. However, the mitochondrial (mt) genome of this fluke has not been known yet. The present study has determined the complete mt genome sequences of E. hortense and assessed the phylogenetic relationships with other digenean species for which the complete mt genome sequences are available in GenBank using concatenated amino acid sequences inferred from 12 protein-coding genes. The mt genome of E. hortense contained 12 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 non-coding region. The length of the mt genome of E. hortense was 14,994 bp, which was somewhat smaller than those of other trematode species. Phylogenetic analyses based on concatenated nucleotide sequence datasets for all 12 protein-coding genes using maximum parsimony (MP) method showed that E. hortense and Hypoderaeum conoideum gathered together, and they were closer to each other than to Fasciolidae and other echinostomatid trematodes. The availability of the complete mt genome sequences of E. hortense provides important genetic markers for diagnostics, population genetics, and evolutionary studies of digeneans.

• 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.

• Journal of Life Science
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• v.21 no.10
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• pp.1452-1459
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• 2011

Citrus is a common term and genus (Citrus) of flowering plants in the rue family, Rutaceae. Citrus is believed to have originated in the part of Southeast Asia bordered by Northeastern India, Myanmar (Burma) and the Yunnan province of China. The taxonomy and systematics of the genus are complex and the precise number of natural species is unclear, as many of the named species are clonally propagated hybrids, and there is genetic evidence that even some wild, true-breeding species are of a hybrid origin. One of the most popular sequences for phylogenetic inference at the generic and infrageneric levels in plants is the chloroplast trnL-trnF region. We evaluated the seven taxa with the trnL-trnF region to estimate phenotypic relationships within the genera Citrus, Poncirus, and Fortunella in Korea. Alignment of the DNA sequences required the addition of numerous gaps. Sequence variation within Citrus was mostly due to insertion/deletion. Within the genus Citrus, C. lomonia and C. sinensis were relatives and sistered with C. aurantium in the four phylogenetic analyses (MP, ML, ME, and NJ). However, some external nodes were poorly supported.

• The Plant Pathology Journal
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• v.34 no.1
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• pp.23-34
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• 2018

The Ralstonia solanacearum species complex (RSSC) can be divided into four phylotypes, and includes phenotypically diverse bacterial strains that cause bacterial wilt on various host plants. This study used 93 RSSC isolates responsible for potato bacterial wilt in Korea, and investigated their phylogenetic relatedness based on the analysis of phylotype, biovar, and host range. Of the 93 isolates, twenty-two were identified as biovar 2, eight as biovar 3, and sixty-three as biovar 4. Applied to the phylotype scheme, biovar 3 and 4 isolates belonged to phylotype I, and biovar 2 isolates belonged to phylotype IV. This classification was consistent with phylogenetic trees based on 16S rRNA and egl gene sequences, in which biovar 3 and 4 isolates clustered to phylotype I, and biovar 2 isolates clustered to phylotype IV. Korean biovar 2 isolates were distinct from biovar 3 and 4 isolates pathologically as well as genetically - all biovar 2 isolates were nonpathogenic to peppers. Additionally, in host-determining assays, we found uncommon strains among biovar 2 of phylotype IV, which were the tomato-nonpathogenic strains. Since tomatoes are known to be highly susceptible to RSSC, to the best of our knowledge this is the first report of tomato-nonpathogenic potato strains. These results imply the potential prevalence of greater RSSC diversity in terms of host range than would be predicted based on phylogenetic analysis.

• Mycobiology
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• v.38 no.1
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• pp.17-25
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• 2010

The common split-gilled mushroom, Schizophyllum commune is found throughout the world on woody plants. This study was initiated to evaluate conditions for favorable vegetative growth and to determine molecular phylogenetic relationship in twelve different strains of S. commune. A suitable temperature for mycelial growth was obtained at $30^{\circ}C$. This mushroom grew well in acidic conditions and pH 5 was the most favorable. Hamada, glucose peptone, Hennerberg, potato dextrose agar and yeast malt extract were favorable media for growing mycelia, while Lilly and glucose tryptone were unfavorable. Dextrin was the best and lactose was the less effective carbon source. The most suitable nitrogen sources were calcium nitrate, glycine, and potassium nitrate, whereas ammonium phosphate and histidine were the least effective for the mycelial growth of S. commune. The genetic diversity of each strain was investigated in order to identify them. The internal transcribed spacer (ITS) regions of rDNA were amplified using PCR. The size of the ITS1 and ITS2 regions of rDNA from the different strains varied from 129 to 143 bp and 241 to 243 bp, respectively. The sequence of ITS1 was more variable than that of ITS2, while the 5.8S sequences were identical. A phylogenetic tree of the ITS region sequences indicated that the selected strains were classified into three clusters. The reciprocal homologies of the ITS region sequences ranged from 99 to 100%. The strains were also analyzed by random amplification of polymorphic DNA (RAPD) with 20 arbitrary primers. Twelve primers efficiently amplified the genomic DNA. The number of amplified bands varied depending on the primers used or the strains tested. The average number of polymorphic bands observed per primer was 4.5. The size of polymorphic fragments was obtained in the range of 0.2 to 2.3 kb. These results indicate that the RAPD technique is well suited for detecting the genetic diversity in the S. commune strains tested.

• BMB Reports
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• v.36 no.5
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• pp.475-487
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• 2003

A gene that encodes a homologue to baculoviral p74, an envelope-associated viral structural protein, has been identified and sequenced on the genome of Choristoneura fumiferana granulovirus (ChfuGV). A part of the ChfuGV p74 gene was located on an 8.9 kb BamHI subgenomic fragment using different sets of degenerated primers. These were designed using the results of the protein sequencing of a major 74 kDa structural protein that is associated with the occlusion-derived virus (ODV). The gene has a 1992 nucleotide (nt) open-reading frame (ORF) that encodes a protein with 663 amino acids with a predicted molecular mass of 74,812 Da. Comparative studies revealed the presence of two major conserved regions in the ChfuGV p74 protein. This study also shows that all of the p74 proteins contain two putative transmembrane domains at their C-terminal segments. At the nucleotide sequence level, two late promoter motifs (TAAG and GTAAG) were located upstream of the first ATG of the p74 gene. The gene contained a canonical poly(A) signal, AATAAA, at its 3' non-translated region. A phylogenetic tree for baculoviral p74 was constructed using a maximum parsimony analysis. The phylogenetic estimation demonstrated that ChfuGV p74 is related the closest to those of Cydia pomonella granulovirus (CpGV) and Phthorimaea operculella granulovirus (PhopGV).

• Journal of fish pathology
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• v.23 no.1
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• pp.1-8
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• 2010

Infectious hematopoietic necrosis virus (IHNV) is the causative agent of IHN, one of the most serious viral diseases of salmonid fish. In this study, glycoprotein (G) gene nucleotide sequence of isolated IHNV RtWanju09 from Jeollabuk-do province was analyzed to evaluate their genetic relatedness to worldwide isolates. As the result, it was revealed that IHNV RtWanju09 isolate belongs to JRt Shizuoka lineage with IHNV RtPy91 and RtJe00. The genetic diversity of G gene between RtWanju09 isolate and RtPy91 isolate from Gangwon-do province was 1.77% and maximum nucleotide diversity among the JRt Shizuoka lineage in Korea was 3.03% during the past 20 years, supporting that the continuous evolution has been occurred among JRt Shizuoka isolates. It was believed that IHNV RtWanju09 isolate has been introduced by the movement of contaminated eggs with IHNV from Gangwon-do to Jeollabuk-do by the reason that the eyed eggs in Jeollabuk-do province used to be obtained from Gangwon-do province. In this study, the domestic transfer of IHNV was firstly investigated by the transfer history of eggs and the phylogenetic analysis using IHNV glycoprotein gene sequence.

• ALGAE
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• v.27 no.2
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• pp.75-82
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• 2012

$Arthrospira$ $platensis$ and $Arthrospira$ $maxima$ are species of cyanobacteria used in health foods, animal feed, food additives, and fine chemicals. This study conducted a comparison of the 16S rRNA gene and $cpcBA$-intergenic spacer ($cpcBA$-IGS) sequences in $Arthrospira$ strains from culture collections around the world. A cluster analysis divided the 10 $Arthrospira$ strains into two main genotypic clusters, designated I and II, where Group I contained $A.$ $platensis$ SAG 86.79, UTEX 2340, $A.$ $maxima$ KCTC AG30054, and SAG 49.88, while Group II contained $A.$ $platensis$ PCC 9108, NIES 39, NIES 46, and SAG 257.80. However, although $A.$ $platensis$ PCC 9223 belonged to Group II-2 based on its $cpcBA$-IGS sequence, this strain also belonged to Group I based on its 16S rRNA gene sequence. Phylogenetic analyses based on the 16S rRNA gene and $cpcBA$-IGS sequences showed no division between $A.$ $platensis$ and $A.$ $maxima$, plus the 16S rRNA gene and $cpcBA$-IGS sequence clusters did not indicate any well-defined geographical distribution, instead overlapping in a rather interesting way. Therefore, the current study supports some previous conclusions based on 16S rRNA gene and $cpcBA$-IGS sequences, which found that $Arthrospira$ taxa are monophyletic. However, when compared with 16S rRNA sequences, $cpcBA$-IGS sequences may be better suited to resolve close relationships and intraspecies variability.

• Journal of Physiology & Pathology in Korean Medicine
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• v.18 no.6
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• pp.1699-1709
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• 2004

Genetic variations and relationship based on the sequences of cpDNA trnL-F gene, nrDNA ITS and ETS region among the twenty four taxa including Panax ginseng C.A. Meyer and its related species were investigated. And taxonomic status and molecular phylogenetic relationship between P. ginseng and related groups were discussed. Molecular systematic data from cpDNA and nrDNA sequences were very useful to elucidate the genetic variations and relationships among the treated taxa. It was found that P. ginseng is the independent unique species with distinct genetic limitation from the related species such as P. quinquefolius, P. japonicum, P. notoginseng and P. pseudoginseng. P. ginseng including cultivated types as well as wild ones formed monophyletic group with high genetic similarities. P. quinquefolius and P. japonicum were the most related sister groups of P. ginseng based on the molecular phylogenetic results in this study.

• Journal of Soil and Groundwater Environment
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• v.25 no.1
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• pp.25-36
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• 2020

In a redox transition zone, geochemical reactions are facilitated by active bacteria that mediate reactions involving electrons, and arsenic (As) and iron (Fe) cycles are the major electron transfer reactions occurring at such a site. In this study, the effect of repetitive redox changes on soil bacterial community in As-contaminated soil was investigated. The results revealed that bacterial community changed actively in response to redox changes, and bacterial diversity gradually decreased as the cycle repeated. Proportion of strict aerobes and anaerobes decreased, while microaerophilic species such as Azospirillum oryzae group became the predominant species, accounting for 72.7% of the total counts after four weeks of incubation. Bacterial species capable of reducing Fe or As (e.g., Clostridium, Desulfitobacterium) belonging to diverse phylogenetic groups were detected. Indices representing richness (i.e., Chao 1) and phylogenetic diversity decreased from 1,868 and 1,926 to 848 and 1,121, respectively. Principle component analysis suggests that repetitive redox fluctuation, rather than oxic or anoxic status itself, is an important factor in determining the change of soil bacterial community, which in turn affects the cycling of As and Fe in redox transition zones.