• Asian-Australasian Journal of Animal Sciences
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• v.33 no.12
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• pp.1896-1904
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• 2020

Objective: Estimating the genetic diversity and structures, both within and among chicken breeds, is critical for the identification and conservation of valuable genetic resources. In chickens, microsatellite (MS) marker polymorphisms have previously been widely used to evaluate these distinctions. Our objective was to analyze the genetic diversity and relationships among 22 chicken breeds in Asia based on allelic frequencies. Methods: We used 469 genomic DNA samples from 22 chicken breeds from eight Asian countries (South Korea, KNG, KNB, KNR, KNW, KNY, KNO; Laos, LYO, LCH, LBB, LOU; Indonesia, INK, INS, ING; Vietnam, VTN, VNH; Mongolia, MGN; Kyrgyzstan, KGPS; Nepal, NPS; Sri Lanka, SBC) and three imported breeds (RIR, Rhode Island Red; WLG, White Leghorn; CON, Cornish). Their genetic diversity and phylogenetic relationships were analyzed using 20 MS markers. Results: In total, 193 alleles were observed across all 20 MS markers, and the number of alleles ranged from 3 (MCW0103) to 20 (LEI0192) with a mean of 9.7 overall. The NPS breed had the highest expected heterozygosity (H_exp, 0.718±0.027) and polymorphism information content (PIC, 0.663±0.030). Additionally, the observed heterozygosity (H_obs) was highest in LCH (0.690±0.039), whereas WLG showed the lowest H_exp (0.372±0.055), H_obs (0.384±0.019), and PIC (0.325±0.049). Nei's DA genetic distance was the closest between VTN and VNH (0.086), and farthest between KNG and MGN (0.503). Principal coordinate analysis showed similar results to the phylogenetic analysis, and three axes explained 56.2% of the variance (axis 1, 19.17%; 2, 18.92%; 3, 18.11%). STRUCTURE analysis revealed that the 22 chicken breeds should be divided into 20 clusters, based on the highest ΔK value (46.92). Conclusion: This study provides a basis for future genetic variation studies and the development of conservation strategies for 22 chicken breeds in Asia.

• Asian-Australasian Journal of Animal Sciences
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• v.29 no.5
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• pp.624-630
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• 2016

Many studies have reported the frequency and distribution of haplogroups among various cattle breeds for verification of their origins and genetic diversity. In this study, 318 complete sequences of the mtDNA control region from four Korean cattle breeds were used for haplogroup classification. 71 polymorphic sites and 66 haplotypes were found in these sequences. Consistent with the genetic patterns in previous reports, four haplogroups (T1, T2, T3, and T4) were identified in Korean cattle breeds. In addition, T1a, T3a, and T3b sub-haplogroups were classified. In the phylogenetic tree, each haplogroup formed an independent cluster. The frequencies of T3, T4, T1 (containing T1a), and T2 were 66%, 16%, 10%, and 8%, respectively. Especially, the T1 haplogroup contained only one haplotype and a sample. All four haplogroups were found in Chikso, Jeju black and Hanwoo. However, only the T3 and T4 haplogroups appeared in Heugu, and most Chikso populations showed a partial of four haplogroups. These results will be useful for stable conservation and efficient management of Korean cattle breeds.

• Korean Journal of Microbiology
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• v.50 no.2
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• pp.152-157
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• 2014

The aim of this study was to investigate the bacterial community inhabited in Callyspongia elegans. Marine bacteria were isolated from the marine sponge C. elegans using marine agar. The resulting 112 isolated pure cultures were then used for further study. They were characterized by determining morphological characteristics through Gram's staining and morphological observation. The colony pigments of bacterial isolates were characterized as yellow, brown, ivory, and white. Thirty-seven strains were found to be Gram-positive and 75 strains were Gram-negative. Seventy-nine strains were coccus-shaped, while 16 strains were rod-shaped. On the basis of the results of the comparative analyses of 16S rDNA gene sequences, the 112 isolated bacteria were divided into 5 major groups: Alphaproteobacteria (39%), Gammaproteobacteria (22%), Actinobacteria (14%), Fimicutes (9%), and Bacteroidetes (6%). It is strongly suggested that fifteen isolates are candidates for a new genera or species, based on the analyses of 16S rDNA gene sequences.

• Journal of Mushroom
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• v.12 no.4
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• pp.251-257
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• 2014

The aim of this study was to analyze the genetic diversity of Hericium species based on their rDNA ITS sequences. Hericium species were collected from various regions and the size of the ITS rRNA gene regions from different Hericium species varied from 450 to 500 bp. A phylogenetic trees based on the ITS region revealed that Hericium species could be classified into 4 different groups, H. erinaceus, H. coralloide, H. alpestre, H. americanum. Among them, ASI 48015 and ASI 48016 was identified as Sprassis and Lentinula genus, respectively, based on blast searches using their rDNA ITS sequences.

• The Journal of Korean Society of Virology
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• v.28 no.4
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• pp.327-335
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• 1998

Hantaan (HTN) and Seoul (SEO) viruses, murid rodent-borne hantaviruses, are known to causes hemorrhagic fever with renal syndrome (HFRS) in Korea. To determine the genomic diversity and molecular phylogeny of HTN and SEO viruses found in Korea, we amplified for part of M and S genomic segments of hantaviruses from sera of HFRS patients and lung tissues of hantavirus seropositive striped-field mice. Both M and S segment of 16 HTN and 2 SEO viruses were amplified by nested reverse transcription-polymerase chain reaction. Based on 324 nucleotides in the M genomic segment, the HTN and SEO strains showed $93.8{\sim}100%$ and $99.1{\sim}99.4%$ homologies, respectively. Similarly, based on 230 nucleotides in the S genomic segment, HTN and SEO strains showed $90.9{\sim}100%$ and 100% homologies, respectively. Phylogenetic analysis of M and S segments indicated that HTN strains could be divided into at least two main groups in M and S trees and the sequence differences detected among the Sand M genomic segments of HTN viruses are consistent with reassortment having taken place between HTN virus strains.

• Journal of Microbiology and Biotechnology
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• v.24 no.12
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• pp.1707-1718
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• 2014

In this study, the phylogenetic diversities of bacterial and archaeal communities in a plant-microbial fuel cell (P-MFC) were investigated together with the environmental parameters, affecting its performance by using rice as a model plant. The beneficial effect of the plant appeared only during a certain period of the rice-growing season, at which point the maximum power density was approximately 3-fold higher with rice plants. The temperature, electrical conductivity (EC), and pH in the cathodic and anodic compartments changed considerably during the rice-growing season, and a higher temperature, reduced difference in pH between the cathodic and anodic compartments, and higher EC were advantageous to the performance of the P-MFC. A 16S rRNA pyrosequencing analysis showed that the 16S rRNAs of Deltaproteobacteria and those of Gammaproteobacteria were enriched on the anodes and the cathodes, respectively, when the electrical circuit was connected. At the species level, the operational taxonomic units (OTUs) related to Rhizobiales, Geobacter, Myxococcus, Deferrisoma, and Desulfobulbus were enriched on the anodes, while an OTU related to Acidiferrobacter thiooxydans occupied the highest proportion on the cathodes and occurred only when the circuit was connected. Furthermore, the connection of the electrical circuit decreased the abundance of 16S rRNAs of acetotrophic methanogens and increased that of hydrogenotrophic methanogens. The control of these physicochemical and microbiological factors is expected to be able to improve the performance of P-MFCs.

• Korean Journal of Plant Taxonomy
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• v.42 no.1
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• pp.13-23
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• 2012

The trnL-F region islocated in the large single-copy region of the chloroplast genome. It consists of the trnL gene, the trnL intron, and the trnL-F IGS. Molecular evolution and phylogenetic relationships in Korean Thalictrum L. were investigated using data from the cpDNA trnL-F region. Bayesian and parsimony analyses of the data set with the gap characteristics recovered well-resolved trees that are topologically similar, with clades supported by some indels evolution. Indel events of cpDNA trnL-F in Korean Thalictrum were interpreted as phylogenetically informative characteristics. Sect. Physocarpum (excluding T. osmorhizoides) was an early-diverging group with in the genus and the remaining section formed strongly supported clades. Korean Thalictrum has various evolutionary patterns, such as the spatial distribution of the nucleotide diversity and transversion-type base substitutions in the trnL-F region.

• Asian-Australasian Journal of Animal Sciences
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• v.17 no.7
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• pp.903-909
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• 2004

The variability of mtDNA hypervariable segment I (HVS I) sequences was investigated in a total of 48 birds belonging to 12 Chinese native chicken breeds. Sixteen haplotypes were identified from 35 polymorphic nucleotide sites which accounted for 6.4% of a sequenced 544 bp fragment. Diversity analysis of the haplotypes showed that Tibetan, Langshan and Henan cockfight chicken had only one haplotype, while ancient haplotypes existed in Taihe silky and Chahua chicken. Phylogenetic analysis of the haplotypes suggested that Chinese native chicken breeds shared 5 maternal lineages and some breeds would share the same maternal lineage, regardless of their external features and ecological types. Both divergent and phylogenetic analysis of the haplotypes indicated the close genetic relationships between the Chinese native chicken breeds and G. g. gallus and G. g. spadiceus from different areas, which implied that G. g. gallus and G. g. spadiceus were the original ancestors of the Chinese native chicken breeds.

• Journal of Species Research
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• v.7 no.1
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• pp.13-23
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• 2018

In 2016, as a part of the research program 'Survey of Korean Indigenous Species', diverse environmental samples were collected from various sources of freshwater, seawater, soil, wetland, reclaimed land, sand, pine forest, plant root, ginseng field, solar saltern, and caves. Thousands of bacterial strains were isolated from the diverse samples and identified based on 16S rRNA gene sequence analyses. The present study, as a phylogenetic subset of the primary research program, reports 24 unrecorded bacterial species in Korea that belong to the orders Rhizobiales and Sphingomonadales in the class Alphaproteobacteria. Based on the high 16S rRNA gene sequence similarities (>98.8%) and formation of a robust phylogenetic clade with the closest type species, it was determined that each strain belonged to each independent and predefined bacterial species. There is no official report that these 24 bacterial species have been described in Korea; therefore, 10 species of nine genera in the order Rhizobiales and 14 species of seven genera in the order Sphingomonadales are described for unreported alphaproteobacterial species in Korea. Gram reaction, colony and cell morphology, biochemical properties, and isolation sources are also provided in the species description section.

• Korean Journal of Poultry Science
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• v.38 no.1
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• pp.5-12
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• 2011

In this study, we analyzed the mitochondrial DNA D-loop region of Korean native chicken to clarify their phylogenetic relationships, possible maternal origin and routes of introduction into Korea. A 1231-1232 bp DNA fragment from the mtDNA D-loop region was sequenced in 315 chickens from 11 populations, Thirty-five variable sites that defined 21 haplotyes were observed. In Korean native chicken, diversity accounted for 90% of the variation, little differentiation among the strains. The 21 haplotypes clustered into 5 clades which were A, B, C, D and E. These results indicate that Korean chickens were derived from China with multiple origins.