• Journal of Life Science
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• v.16 no.5
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• pp.740-745
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• 2006

Inter simple sequence repeat (ISSR) markers were performed in order to analyse the phylogenetic relationships of four taxa of Castor-aralia (Kalopanax pictus): K. pictus, K. pictus var. magnificus, K. pictus var. maximowiczii, and thornless K. pictus. The 11 primers were produced 64 reproducible ISSR bands. Analysis of ISSR from individual plants of Korean K. pictus resulted in 41 polymorphic bands with 64.1%. When species were grouped by four taxa, within group diversity was 0.115 $(H_S)$, while among group diversity was 0.467 $(G_{ST})$ on a per locus basis. The estimated gene flow (Nm) for K. pictus var. maximowiczii and K. pictus var. magnificus were very higher than K. pictus. It is suggested that the isolation of geographical distance and reproductive isolation among K. pictus populations may have played roles in shaping the population structure of this species. In phenetic tree, ISSR markers are very effective in classifying natural populations as well as taxon levels of genus Kalopanax in Korea.

• Korean Journal of Microbiology
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• v.37 no.1
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• pp.49-55
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• 2001

Bacillus anthracis is a gram-positive spore-forming bacterium that causes the disease anthrax. The anthrax toxin contains three components, including the protective antigen (PA), which binds to eucaryotic cell surface receptors and mediates the transport of toxins into the cell. In this study, the entire 2,294-nucleotide protective antigen gene (pag) was sequenced from 4 of B. anthracis strains to identify potential variation in the toxin and to further our understanding of B. anthracis evolution in Korea. Sequence alignment of the entire PA gene from 30 strains representative of the four B. anthracis diversity groups revealed mutations. The mutation of B. anthracis BAK are located adjacent to a highly antigenic region crossing the junction between PA domains 3 and 4 shown to be critical to LF binding. The different mutational combinations observed in this study give rise to 11 PA genotypes and 4PA phenotypes. Three-dimensional analysis of all the amino acid changes (Ala to Val) observed in BAK indicated that these changes are not only close sequentially but also very close in three-dimensional space to the antigenic region importan tfor LF binding. Phylogenetic (cladistic) analysis of the pag corresponded with previous strain grouping based on chromosomal variation, suggesting that plasmid evolution in B. anthracis has occurred with little or no horizontal transfer between the different strains.

• Korean Journal of Microbiology
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• v.51 no.2
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• pp.148-155
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• 2015

The diversity of endobacteria in the edible part (cap and stipe) king oyster mushroom (Pleurotus eryngii) was investigated using 16S rRNA sequence analysis. The bacterial 16S rRNA libraries were constructed from the body cap (BC) and the body stipe (BS) of the king oyster mushroom. The twenty sequenced BC clones were divided into four groups and the largest group was affiliated with the Firmicutes (40% of clones). While, the twenty sequenced BS clones could be divided into six groups and the largest group was affiliated with the Actinobacteria (40% of clones). The predominant bacterial family from both the cap and stipe of the mushroom was corresponded with the Gram positive bacteria (62.5%).

• The Korean Journal of Mycology
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• v.43 no.2
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• pp.92-98
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• 2015

Hydrocharis dubia Backer and Salvinia natans All. were sampled from the Junam and Dongpan reservoirs, representative freshwater wetlands of Korea. A total of 19 endophytic fungal strains were isolated from hydrophytes native to the Junam wetlands and 5 strains were isolated from the Dongpan wetlands. Depending on phylogenetic analysis based on internal transcribed spacer (ITS) region, strains from Junam belonged to 11 genera and from Dongpan belonged to 5 genera. Fusarium, Phoma and Talaromyces were commonly distributed genera from two wetlands. The fungal diversity index showed clear differences between each wetlands or each host hydrophyte. Above all, the highest diversity value was observed from Salvinia natans All., which have been reported as promising biological resources as eutrophication controller in environmental ecology.

• Korean Journal of Microbiology
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• v.46 no.3
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• pp.255-261
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• 2010

The bacterial community structure associated with two marine sponges, Hyrtios sp. 604 and Callyspongia sp. 612 collected from the South Pacific Ocean were analyzed by 16S rDNA-denaturing gradient gel electrophoresis (DGGE). The phylogenetic analysis showed that the bacterial community associated with Hyrtios sp. 604 contained diverse bacterial groups such as Chloroflexi, Firmicutes, Cyanobacteria, Alphaproteobacteria, Gammaproteobacteria, Actinobacteria, and Acidobacteria. Callyspongia sp. 612 harbored Chloroflexi, Cyanobacteria, Alphaproteobacteria, and Gammaproteobacteria. Hyrtios sp. 604 belonging to genus Hyrtios known to produce natural products showed greater bacterial diversity than Callyspongia sp. 612. Phylum Actinobacteria was shown to be one of dominant bacterial groups in Hyrtios sp. 604. Although the same phyla of bacteria were found in both sponge species, the spongeassociated predominant bacterial groups differed between the two sponges with different chemical characteristics from the same geographical location. Uncultured bacteria represented over 90% of the bacteria diversity present in all bacterial communities of the sponges.

• Korean Journal of Plant Resources
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• v.24 no.6
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• pp.702-711
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• 2011

Buckwheat (Fagopyrum esculentum Moench), one of the minor crops grown in Korea belonging to the Polygonaceae family, is an annual crop widely cultivated in Asia, Europe, and America and has a character of outcrossing and self-incompatibility. The objective of this study was to analyze the genetic variability, phylogenetic relationships and population structure of buckwheat landraces of Korea using SSR markers. Ten microsatellite markers have been detected from a total of 79 alleles among the 179 buckwheat accessions were collected from Korea. The number of allele per marker locus ($N_A$) ranged from 2 (GB-FE-001, GB-FE-043 and GB-FE-055) to 31 (GB-FE-035) with an average of 7.9 alleles. GB-FE-035 was the most polymorphic with the highest PIC value 0.93. Major allele frequencies ($M_{AF}$) for the 10 polymorphic loci varied from 0.12 to 0.97 with a mean allele frequency of 0.57. The expected heterozygosity ($H_E$) values ranged from 0.05 to 0.94 with an average of 0.53. The observed heterozygosity ($H_O$) ranged from 0.06 to 0.92 with an average of 0.42. The overall polymorphic information contents (PIC) values ranged from 0.05 to 0.93 with an average of 0.48. The landrace accessions of buckwheat used in the present study were not distinctly grouped according to geographic distribution. The study concludes that the results revealed genetic differentiation was low according to the geographic region because of outcrossing and self-incompatibility. We reported that our analyses on the genetic diversity of common buckwheat cultivars of Korea were performed by using of microsatellite markers.

• Journal of Animal Science and Technology
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• v.63 no.2
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• pp.248-261
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• 2021

Attributable to their major function in pathogen recognition, the use of bovine leukocyte antigens (BoLA) as disease markers in immunological traits in cattle is well established. However, limited report exists on polymorphism of the BoLA gene in zebu cattle breeds by high resolution typing methods. Thus, we used a polymerase chain reaction sequence-based typing (PCR-SBT) method to sequence exon 2 of the BoLA class II DRB3 gene from 100 animals (Boran, n = 13; Sheko, n = 20; Fogera, n = 16; Horro, n = 19), Hanwoo cattle (n = 18) and Bangladesh Red Chittagong zebu (n = 14). Out of the 59 detected alleles, 43 were already deposited under the Immuno Polymorphism Database for major histocompatibility complex (IPD-MHC) while 16 were unique to this study. Assessment of the level of genetic variability at the population and sequence levels with genetic distance in the breeds considered in this study showed that Zebu breeds had a gene diversity score greater than 0.752, nucleotide diversity score greater than 0.152, and mean number of pairwise differences higher than 14, being very comparable to those investigated for other cattle breeds. Regarding neutrality tests analyzed, we investigated that all the breeds except Hanwoo had an excess number of alleles and could be expected from a recent population expansion or genetic hitchhiking. Howbeit, the observed heterozygosity was not significantly (p < 0.05) higher than the expected heterozygosity. The Hardy Weinberg equilibrium (HWE) analysis revealed non-significant excess of heterozygote animals, indicative of plausible over-dominant selection. The pairwise FST values suggested a low genetic variation among all the breeds (FST = 0.056; p < 0.05), besides the rooting from the evolutionary or domestication history of the cattle. No detached clade was observed in the evolutionary divergence study of the BoLA-DRB3 gene, inferred from the phylogenetic tree based on the maximum likelihood model. The investigation herein indicated the clear differences in BoLA-DRB3 gene variability between African and Asian cattle breeds.

• Journal of Species Research
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• v.12 no.4
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• pp.281-285
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• 2023

The red-tongue viper(Gloydius ussuriensis) is one of only three species of the genus Gloydius found in South Korea. Gloydius ussuriensis has a narrow activity radius and is distributed nationwide, and this species was reported to have the largest population among the Korean species in genus Gloydius. Preliminary results of a phylogenetic analysis using part of the mitochondrial DNA indicated that domestic G. ussuriensis is not comprised of monophyletic groups, and morphological analysis showed differences between domestic populations. In this study, we developed 17 microsatellites for the analysis of G. ussuriensis genetic diversity based on these characteristics. These microsatellites were developed using six multiplex panels, which could be employed to validate 80 G. ussuriensis specimens from different geographical regions in South Korea. The average number of alleles per locus was 12.2 and ranged from 4 to 25 alleles; the observed heterozygosity ranged from 0.238 to 0.950 and the expected heterozygosity ranged from 0.213 to 0.933. As a result of assessing four inland populations, a high level of genetic diversity was confirmed. These newly developed markers will be useful for further studies on the population structure and evolutionary history of the G. ussuriensis.

• Korean Journal of Ecology and Environment
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• v.53 no.3
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• pp.265-274
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• 2020

Silver croaker (Pennahia argentata) is a turbulent species that is widely distributed worldwide and is mainly found in the bottom of the ocean. In the study, we characterized the cytochrome c oxidase subunit I (COI) gene of the mitochondrial DNA (mtDNA) on P. argentata inhabiting Gwangyang Bay and analyzed the phylogenetic location of marine fish species. As a result of multiple arrangement of 605 bp COI sequences, high homology of mtDNA nucleotide sequences was confirmed in the silver croakers from Gwangyang Bay (98~100%). However, the nucleotide variation was different according to the catching points of the inland and the open seas of Gwangyang Bay. The nucleotide sequence variation in COI was high in P. argentata from the open seas of Gwangyang Bay (43.2~70.3%). Furthermore, the phylogenetic analysis of 13 fish showed that P. argentata from Gwangyang Bay were grouped into one clade with P. argentata reported in Taiwan, and the evolutionary distance was 0.036. In addition, it was identified that the evolutionary distance was close to that of fish belonging to the Mi-iuy croaker (Miichthys miiuy) and the Big-head pennah croaker (Pennahia Macrocephalus) (0.041~0.048). The result of these studies will be used as the key genetic information for fisheries resources monitoring and species diversity management according to the coastal environment.

• Animal Bioscience
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• v.34 no.4
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• pp.525-532
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• 2021

Objective: Old World camels are a valuable genetic resource for many countries around the world due to their adaptation to the desert environment. At present, Old World camels have encountered the challenge of unprecedented loss of genetic resources. Through our research, we would reveal the population structure and genetic variation in Old World camel populations, which provides a theoretical basis for understanding the germplasm resources and origin and evolution of different Old World camel populations. Methods: In the present study, we assessed mtDNA control region sequences of 182 individuals from Old World camels to unravel genetic diversity, phylogeography, and demographic dynamics. Results: Thirty-two haplotypes confirmed by 54 polymorphic sites were identified in the 156 sequences, which included 129 domestic and 27 wild Bactrian camels. Meanwhile, 14 haplotypes were defined by 47 polymorphic sites from 26 sequences in the dromedaries. The wild Bactrian camel population showed the lowest haplotype and nucleotide diversity, while the dromedaries investigated had the highest. The phylogenetic analysis suggests that there are several shared haplotypes in different Bactrian camel populations, and that there has been genetic introgression between domestic Bactrian camels and dromedaries. In addition, positive values of Tajima's D and Fu's Fs test demonstrated a decrease in population size and/or balancing selection in the wild Bactrian camel population. In contrast, the negative values of Tajima's D and Fu's Fs test in East Asian Bactrian camel populations explained the demographic expansion and/or positive selection. Conclusion: In summary, we report novel information regarding the genetic diversity, population structure and demographic dynamics of Old World camels. The findings obtained from the present study reveal that abundant genetic diversity occurs in domestic Bactrian camel populations and dromedaries, while there are low levels of haplotype and nucleotide diversity in the wild Bactrian camel population.