• Journal of Species Research
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• v.7 no.3
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• pp.202-209
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• 2018

Eight bacterial strains, 18JY8-13, 18JY13-16, 18JY43-7, 18JY12-7, 18JY1-1, 18JY1-7, 18JY15-3, and 18JY7-2 assigned to the phylum Firmicutes were isolated from a variety of soil samples collected in the Jeju Island, Korea. Cells of the eight strains were Gram-positive, aerobic and showed resistant to UV-radiation. Phylogenetic analysis based on 16S rRNA gene sequence revealed that strains 18JY8-13, 18JY13-16, 18JY43-7, 18JY12-7, 18JY1-1, 18JY1-7, 18JY15-3, and 18JY7-2 were most closely related to Bacillus paranthracis(99.9%), Bacillus paramycoides(99.6%), Bacillus australimaris(99.9%), Bacillus wiedmannii (100%), Bacillus halosaccharovorans(99.6%), Bacillus deserti(98.7%), Bacillus cereus (99.8%), and Bacillus albus(100%), respectively. This is the first report of these eight species in Korea.

• Journal of Species Research
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• v.7 no.3
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• pp.210-221
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• 2018

Eight bacterial strains assigned to the phylum Firmicutes were isolated from the soil samples in Korea. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains 18JY14-16, 18JY14-35, 18JY42-5, 18JY12-20, 18JY35-8, 18JY76-9, 18JY39-1 and 18JY54-12 were most closely related to Paenibacillus lupini (MH497638; 99.4%), Paenibacillus illinoisensis (MH497643; 99.8%), Paenibacillus tundrae (MH497658; 99.7%), Paenibacillus selenitireducens (MH497639; 99.4%), Paenibacillus eucommiae (MH 497640; 99.9%), Paenibacillus vini (MH497654; 99.4%), Paenibacillus gorillae (MH497647; 99.5%), and Paenibacillus macquariensis (MH497649; 99.9%) respectively. These Paenibacillus species were Gram-stain-positive, rod-shaped and radiation resistant bacteria. This is the first report of these nine bacterial species in Korea.

• Journal of Species Research
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• v.7 no.3
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• pp.222-230
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• 2018

Six bacterial strains 18JY42-3, 18SH, 18JY76-11, 17J11-11, 18JY14-14, and 18JY15-11 assigned to the phylum Proteobacteria, Firmicutes, and Actinobacteria were isolated from soil samples in Korea. The Cohnella species, strain 18JY42-3 was Gram-stain-positive, short rod-shaped and beige-colored. The Methylobacterium species, strains 18SH and 18JY76-11 were Gram-stain-negative, short rod-shaped and pink-colored. The Microterricola species, strain 17J11-11 was Gram-stain-positive, short rod-shaped and yellow-colored. The Paenarthrobacter species, strains 18JY14-14 and 18JY15-11 were Gram-stain-positive, short rod-shaped and white-colored. Phylogenetic analysis based on 16S rRNA gene sequence showed that strains 18JY42-3, 18SH, 18JY76-11, 17J11-11, 18JY14-14, and 18JY15-11 were most closely related Cohnella rhizosphaerae (MH497628; 98.8%), Methylobacterium goesingense (MH497632; 99.1%), Methylobacterium populi (MH497635; 99.9%), Microterricolagilva (MH504108; 98.4%), Paenarthrobacter nicotinovorans (MH497641; 100%), and Paenarthrobacter nitroguajacolicus (MH497646; 99.2%), respectively. All the six unrecorded strains showed resistance to UV radiation. This is the first report of these six species in Korea.

• Journal of Species Research
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• v.9 no.2
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• pp.85-104
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• 2020

In 2019, after a comprehensive investigation of indigenous prokaryotic species in Korea, a total of 12 bacterial strains assigned to the phylum Proteobacteria were isolated from soil. With the high 16S rRNA gene sequence similarity (>98.8%) and formation of a robust phylogenetic clade with the closest species, it was determined that each strain belonged to independent, predefined bacterial species. This study identified two species in the family Burkholderiaceae, one species in the family Comamonadaceae, two species in the family Oxalobacteraceae, one species in the family Micrococcaceae, one species in the family Bradyrhizobiaceae, one species in the family Methylobacteriaceae, one species in the family Rhizobiaceae, one species in the family Rhodocyclaceae, and one species in the family Sphingomonadaceae. There is no official report about these 12 species in Korea, so are described as unreported bacterial species in Korea in this study. Gram reaction, basic biochemical characteristics, colony, and cell morphology are also described in the species description section.

• Journal of Life Science
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• v.22 no.3
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• pp.285-292
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• 2012

Genus Spiraea is composed of many long-lived woody species that are primarily distributed throughout Asia and Europe. In this study, we evaluated a representative sample of the 38 taxa in the world, including 14 in Korea, with nuclear ribosomal DNA internal transcribed spacer sequences (ITS) to estimate genetic relationships within the genus. The molecular data allowed us to resolve well-supported clades in the taxa. In 47 world accessions (38 taxa: 14 Korean taxa, 33 world taxa, and 9 overlapping taxa), total alignment length was 689 positions, of which 452 were parsimony informative, 527 variable, 75 singleton, and 159 constant characters. Although the phylogenic tree showed that many taxa of genus Spiraea were well separated from each other, many branches were not congruent with the morphological characteristics and geographical distributions of the genus. There were 430 segregating sites and the nucleotide diversity (${\pi}$) value was 0.281. Under the neutral mutation hypothesis, the probability that the Tajima test statistic (D) is positive (2.325) is more than 0.5. Therefore, there may be a site at which natural selection, which increases genetic variation, is operating.

• Journal of Life Science
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• v.23 no.11
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• pp.1305-1310
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• 2013

Dill (Anethum graveolens L.) is an annual herb with a long history and it is mainly used as a spice and as a medicine that is effective as a digestive aid, a sedative, and a narcotic, and that helps remove bad breath. Dill grows wild in the districts along the shores of the Mediterranean Sea, West Asia, China, and Korea. An estimate of the phylogenetic relationships within dill accessions in 20 countries was inferred using data from the rps16-trnK3-intergenic spacer. The aligned data sets for dill ranged from 747 to 779 nucleotides (bp) as a result of the differences in the insert/delete nucleotides. The sequence variation within the dill accessions was mostly due to nucleotide substitutions, although several small insertions and deletions can be found. Among 100 accessions from 20 countries, the Eastern Asia accessions were more closely related to the North American accessions than to the Central Asia and European accessions. Although some accessions were not congruent completely with geographical locations, the dill accessions with rps16-trnK analysis resulted in plants with better-resolved clades.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.54 no.5
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• pp.685-690
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• 2021

Harmful shell-boring species of the genus Polydora (Polychaeta: Spionidae) were frequently reported from commercially important mollusk species in Korea, Japan and China. The traditional approach based on the morphological characteristics showed limitations for species discrimination among shell-boring species. Therefore, DNA barcoding was adopted to identify Polydora species using molecular markers. Two Polydora species (P. haswelli and P. hoplura) in abalone shells were reported from our previous molecular phylogenetic study. In this study, we additionally reported the presence of shell-boring Polydora haswelli in commercially sold shellfish. The taxon-specific cox1 marker used in this study successfully allowed the isolation of P. haswelli from cockle Scapharca subcrenata, mussel Mytilus galloprovincialis, oyster Crassostrea gigas and scallop Argopecten irradians. Polydora hoplura was not found in these shellfish species. The genetic variations were found on the intraspecific level of P. haswelli and the same genotype was also detected in different shellfish species. This result can provide information on a new host and accurate parasitic Polydora species. Moreover, this report can be used as the biodiversity data of Polydora species on the invasion and transition of harmful Polydora species in mollusk aquaculture farms.

• Journal of Microbiology and Biotechnology
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• v.31 no.4
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• pp.520-528
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• 2021

Plesiomonas shigelloides, a member of the family Vibrionaceae, is a gram-negative, rod-shaped, facultative anaerobic bacterium with flagella. P. shigelloides has been isolated from such sources as freshwater, surface water, and many wild and domestic animals. P. shigelloides contains 102 O-antigens and 51 H-antigens. The diversity of O-antigen gene clusters is relatively poorly understood. In addition to O1 and O17 reported by other laboratories, and the 12 O serogroups (O2, O10, O12, O23, O25, O26, O32, O33, O34, O66, O75, and O76) reported previously by us, in the present study, nine new P. shigelloides serogroups (O8, O17, O18, O37, O38, O39, O44, O45, and O61) were sequenced and annotated. The genes for the O-antigens of these nine groups are clustered together in the chromosome between rep and aqpZ. Only O38 possesses the wzm and wzt genes for the synthesis and translocation of O-antigens via the ATP-binding cassette (ABC) transporter pathway; the other eight use the Wzx/Wzy pathway. Phylogenetic analysis using wzx and wzy showed that both genes are diversified. Among the nine new P. shigelloides serogroups, eight use wzx/wzy genes as targets. In addition, we developed an O-antigen-specific PCR assay to detect these nine distinct serogroups with no cross reactions among them.

• Plant Breeding and Biotechnology
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• v.6 no.4
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• pp.321-336
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• 2018

Sesame (Sesamum indicum L.) is an important oilseed crop grown in tropical and subtropical areas. The objective of this study was to investigate the genetic relationships among 129 sesame landraces and cultivars using simple sequence repeat (SSR) markers. Out of 70 SSRs, 23 were found to be informative and produced 157 alleles. The number of alleles per locus ranged from 3 - 14, whereas polymorphic information content ranged from 0.33 - 0.86. A distance-based phylogenetic analysis revealed two major and six minor clusters. The population structure analysis using a Bayesian model-based program in STRUCTURE 2.3.4 divided 129 sesame accessions into three major populations (K = 3). Based on pairwise comparison estimates, Pop1 was observed to be genetically close to Pop2 with $F_{ST}$ value of 0.15, while Pop2 and Pop3 were genetically closest with $F_{ST}$ value of 0.08. Analysis of molecular variance revealed a high percentage of variability among individuals within populations (85.84%) than among the populations (14.16%). Similarly, a high variance was observed among the individuals within the country of origins (90.45%) than between the countries of origins. The grouping of genotypes in clusters was not related to their geographic origin indicating considerable gene flow among sesame genotypes across the selected geographic regions. The SSR markers used in the present study were able to distinguish closely linked sesame genotypes, thereby showing their usefulness in assessing the potentially important source of genetic variation. These markers can be used for future sesame varietal classification, conservation, and other breeding purposes.

• Parasites, Hosts and Diseases
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• v.56 no.6
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• pp.559-565
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• 2018

The identification and characterization of pathogenic and zoonotic tick-borne diseases like granulocytic anaplasmosis are essential for developing effective control programs. The differential diagnosis of pathogenic Anaplasma phagocytophilum and non-pathogenic A. phagocytophilum-like Anaplasma spp. is important for implementing effective treatment from control programs. The objective of the present study was to investigate the prevalence of Anaplasma spp. in horses in Korea by nucleotide sequencing and restriction enzyme fragment length polymorphism assay. Of the 627 horses included in the study, only 1 (0.2%) was infected with A. phagocytophilum. Co-infection with A. phagocytophilumlike Anaplasma spp. was not detected in the study. The 16S rRNA sequence of A. phagocytophilum was similar (99.5-100%) to A. phagocytophilum 16S rRNA isolated from horses in other countries. PCR adapted to amplify A. phagocytophilum groEL and msp2 genes failed to generate amplicons, suggesting genetic diversity in these genes. This study is the first molecular detection of A. phagocytophilum in horses in Korea. Human granulocytic anaplasmosis and animal infection of A. phagocytophilum have been reported in Korea recently. Because of vector tick distribution, global warming, and the increase of the horse industry, horses should be considered as a potential reservoir for A. phagocytophilum, and cross infectivity should be evaluated even though a low prevalence of infection was detected in this study. Furthermore, continuous surveillance and effective control measures for A. phagocytophilum should be established to prevent disease distribution and possible transmission to humans.