• The Sea:JOURNAL OF THE KOREAN SOCIETY OF OCEANOGRAPHY
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• v.18 no.3
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• pp.131-141
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• 2013

Stock identification of Todarodes pacificus collected in the East Sea, Yellow Sea and East China Sea during the period from September to December in 2011 was analyzed by morphometric characters and mitochondrial DNA (mtDNA) cytochrome oxidase subunit I (COI) gene nucleotide variations. Frequency distributions of mantle length was analyzed by morphological method with measuring size of T. pacificus. Then each stock was estimated to confirm their maturation for mean mantle length comparing with mean mature mantle length 20-22 cm. According to morphologic stock identification, it is estimated that the northern part of East Sea is categorized as summer stock and the rest parts, including mid /southern part of the East Sea, northern part of the East China Sea and northern part of the West Sea were autumn stock. For genetic analysis, a total 49 haplotypes were defined by 33 variable nucleotide sites. From the extensive haplotype diversity, limited nucleotide diversity and star-like shape of haplotype network, T. pacificus appears to have undergone rapid population expansion from an ancestral population with a small effective population size. Although pair-wise Fst estimates which represent genetic difference among groups were low, there are relatively remarkable difference of Fst between middle and southern part of the East Sea. Although middle part of the East Sea and southern part of the East Sea were situated at the East Sea, genetically separated groups were appeared.

• Journal of Life Science
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• v.27 no.7
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• pp.746-753
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• 2017

In order to rapidly identify four drums species, Larimichthys polyactis, L. crocea, Atrobucca nibe, and Pseudotolithus elongates, a highly efficient and quick method has been developed using multiplex polymerase chain reaction (PCR) with species-specific primers. Around 1.4 kbp of the mitochondrial COI gene sequences from the four drums species were aligned, and species-specific forward primers were designed, based on the single nucleotide polymorphism (SNP). The optimal conditions for PCR amplification were selected through cross-reactivity, using a gradient PCR method. The PCR results demonstrated species-specific amplification for each species at annealing temperatures between 50 and $62^{\circ}C$. Multiplex species-specific PCR (MSS-PCR) amplification reactions with four pairs of primers were performed for sixteen specimens of each species. MSS-PCR lead to a species-specific amplification of a 1,540 bp fragment in L. polyactis, 1,013 bp in A. nibe, 474 bp in L. crocea, and 182 bp in P. elongates, respectively. The four different sizes of each PCR product can be quickly and easily detected by single gel electrophoresis. The sensitivity of the MSS-PCR of the DNA was up to $0.1ng/{\mu}l$ as a starting concentration for the four different species tested. These results suggest that MSS-PCR, with species-specific primers based on SNP, can be a powerful tool in the rapid identification of the four drums species, L. polyactis, L. crocea, A. nibe, and P. elongates.

• Korean Journal of Environmental Biology
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• v.41 no.3
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• pp.325-334
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• 2023

The invasive red swamp crayfish, Procambarus clarkii, is native to south-central United States and northeastern Mexico. Recently, it has been being spreading in the wild in South Korea. However, its primary sources, introduction routes, establishment, and expansion in South Korea remain unclear. Here, we analyzed genetic diversity and population genetic structures of its domestic natural populations during early invasion, commercial stock from local aquaria (a suspected introduction source), and original United States population using mitochondrial COI gene sequences for 267 individuals and eight microsatellite markers for 158 individuals. Natural and commercial populations of P. clarkii showed reduced genetic diversity (e.g., haplotype diversity and allelic richness). The highest genetic diversity was observed in one original source population based on both genetic markers. Despite a large number of individuals in commercial aquaria, we detected remarkably low genetic diversity and only three haplotypes among 226 individuals, suggesting an inbred population likely originating from a small founder group. Additionally, the low genetic diversity in the natural population indicates a small effective population size during early establishment of P. clarkii in South Korea. Interestingly, genetic differentiation between natural populations and the United States population was lower than that between natural populations and aquarium populations. This suggests that various genetic types from the United States likely have entered different domestic aquariums, leading to distinct natural populations through separate pathways. Results of our study will provide an insight on the level of genetic divergence and population differentiation during the initial stage of invasion of non-indigenous species into new environments.

• Journal of Food Hygiene and Safety
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• v.27 no.3
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• pp.317-324
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• 2012

In order to determine an authenticity of food ingredient, we used DNA barcode method by universal primers. For identification of animal food ingredients, LCO1490/HCO2198 and VF2/FISH R2 designed for amplifying cytochrome c oxidase subunit1 (CO1) region and L14724/H15915 for cytochrome b (cyt b) region on mitochondrial DNA were used. Livestock (cow, pig, goat, sheep, a horse and deer) was amplified by LCO1490/HCO 2198, VF2/FISH R2 and L14724/H15915 primers. Poultry (chicken, duck, turkey and ostrich) was amplified by LCO1490/HCO 2198 and VF2/FISH R2 primers. But, Fishes (walleye pollack, herring, codfish, blue codfish, trout, tuna and rockfish) were only amplified by VF2/FISH R2 primers. For plant food ingredients, 3 types of primers (trnH/psbA, rpoB 1F/4R and rbcL 1F/724R) have been used an intergenic spacer, a RNA polymerase beta subunit and a ribulose bisphosphate carboxylase region on plastid, respectively. Garlic, onion, radish, green tea and spinach were amplified by trnH/psbA, rpoB 1F/4R and rbcL 1F/724R. The PCR product sizes were same by rpoB 1F/4R and rbcL 1F/724R but, the PCR product size using trnH/psbA primer was different with others for plants each. We established PCR condition and universal primer selection for 17 item's raw materials for foods and determine base sequences aim to PCR products in this study. This study can apply to determine an authenticity of foods through making an comparison between databases and base sequences in gene bank. Therefore, DNA barcode method using universal primers can be a useful for species identification techniques not only raw materials but also processed foods that are difficult to analyze by chemical analysis.

• Journal of Life Science
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• v.18 no.7
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• pp.1015-1018
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• 2008

To analyze the population genetic structure of the oyster Crassostrea gigas Thunberg, 34 specimens werecollected from Gamak bay in March, 2007. Total genomic DNA was extracted from each sample and PCR was performed to identify haplotypes of oyster by using HCO2918 and LCO1491 primers. Four kinds of haplotypes (CR1, CR2, CR3, and CR4) were identified. Among these group, CR3 showed the highest relative frequency at 73% than any other of haplotypes. On the basis of hierarchical genetic structure, the population of Gamak showed a higher genetic relationship with Namhae, but the genetic distance between southern and western coasts was negative and no statistical significance was found (p>0.05). Consequently, the oyster from Korea coast is determined to be both homogenous and large.

• Journal of Ecology and Environment
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• v.36 no.4
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• pp.449-463
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• 2013

DNA barcoding is becoming a widely applied tool to accurately discriminate red algae. We tested the effectiveness of DNA barcoding for identification and discovery of Champia species in Korea and clarified the phylogenetic relationships using the plastid rbcL gene. As results, we described four species of Champia such as C. inkyua sp. nov., C. recta Noda, C. bifida Okamura, and C. expansa Yendo. A new species, C. inkyua, is characterized by entangled thallus, terete and irregular branches, hooked apices, and longitudinal filaments running throughout the frond periphery only. Longitudinal filaments were composed of a complete cell with two half cells between diaphragms in the cavity. C. recta and C. bifida were reinstated with previously used names of C. parvula and C. compressa, respectively. C. recta is the first recorded species from Korea and is characterized by an erect thallus, terete and irregular branches, and straight apices. C. bifida is characterized by compressed thallus, pinnate or alternate branches, and bifid apices. C. expansa is characterized by flabellate thallus and dichotomous branches. Molecular analyses of COI and rbcL genes revealed sufficient sequence divergence to warrant species recognition in the genus Champia.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.50 no.6
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• pp.829-836
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• 2017

This study investigated the species composition and abundance of floating fish eggs to determine the timing and location of spawning of fish inhabiting the coastal waters of Sagye, Jejudo Island. Eggs were collected with a Bongo net bimonthly from May 2009 to February 2010. Identifications were based on nucleotide sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene. Eggs were determined to belong to 43 distinct taxa, 35 of which were identified to the species level. The assemblage spanned eight orders, 23 families, and 32 genera. The number of taxa collected varied from month to month, with 14 taxa (12 species) found in June 2009, 11 taxa (10 species) in October 2009, 10 taxa (nine species) each in August 2009 and February 2010, eight taxa (six species) in April 2009, and five taxa (four species) in December 2009. Five abundant species (Branchiostegus japonicus, Engraulis japonicus, Pseudolabrus sieboldi, Goniistius zonatus, and Halichoeres tenuispinis) together represented 52.8% of the total number of eggs collected during the study.

• Journal of Species Research
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• v.4 no.1
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• pp.1-22
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• 2015

Surveys of easily accessible or moderately remote South Korean mountains has revealed several common exotic and early species-complexes [Amynthas corticis (Kinberg, 1867) with A. diffringens (Baird, 1869), A. gracilis (Kinberg, 1867) and Metaphire californica (Kinberg, 1867)], plus an unexpected number of new native taxa. Megascolecid Metaphire muuido sp. nov. and lumbricid Eisenia muuido sp. nov. are newly described from Muuido Island, Incheon. Montane taxa are parthenogenetic Amynthas tokioensis oculo sub-sp. nov. that lacks male pores but is yet comparable to both Amynthas tokioensis (Beddard, 1892) and Metaphire soulensis (Kobayashi, 1938) with its possible new synonym A. chiakensis Hong & James, 2013. Apparently unique sympatric taxa are Amynthas bangtaesan bangtaesan and A. b. confinius sup-spp. nov., Amynthas centurio sp. nov., Amynthas punicans sp. nov., Amynthas seoraksan and A. seoraksan iti sub-spp. nov. These are newly described and their DNA COI gene barcodes, where obtainable, are presented in a phylogram with outgroup Acanthodrilidae Microscolex dubius (Fletcher, 1887) from Lake Biwa Japan being a new exotic record for Asia.

• Proceedings of the National Institute of Ecology of the Republic of Korea
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• v.1 no.1
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• pp.52-57
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• 2020

Bacterial symbionts are common across insects, including ants (Hymenoptera: Formicidae). Reproduction-manipulating endosymbionts, such as Wolbachia, Spiroplasma, Rickettsia, and Cardinium, are closely associated with many aspects of host-insect life. In addition, phage WO plays an essential role in the phenotypic effects of Wolbachia. Although endosymbionts are possible biological control agents, there is a lack of knowledge of their rate of infection of ants in Korea. We tested a range of Korean ant species for the presence of Wolbachia, Spiroplasma, Rickettsia, Cardinium, and phage WO by extracting DNA from the ants and using specific primer sets to test the status of infections. In addition, the mitochondrial cytochrome c oxidase I (COI) gene of the host ants was amplified to confirm the molecular identification and phylogenetic relationship between the hosts. We found that infection with Wolbachia (29.6% of species) is relatively common when compared with that of other endosymbionts. Only one species was infected with Spiroplasma. Infection with Rickettsia and Cardinium was not detected in the examined ants. Most Wolbachia in ants were infected with phage WO. Although the phenotypic effects of endosymbionts in ants are still unknown, this first survey of endosymbionts in Korea is the first step toward the use of reproduction-manipulating endosymbionts.

• ALGAE
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• v.36 no.3
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• pp.155-163
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• 2021

The crustose brown algal genus Endoplura has been known as a monotypic genus characterized by its intercalary plurangial reproductive structures composed of 2-4 separate parallel filaments terminated by 2-5 sterile cells and by containing several to many chloroplasts per cell. In this study, Endoplura jejuensis sp. nov. and E. koreana sp. nov. from Korea are newly described based on molecular and morphological analyses. Our phylogenetic analyses of the rbcL gene reveal that E. jejuensis sp. nov. and E. koreana sp. nov. are placed in the same clade with "E. aurea" from Japan with a strong bootstrap supporting value. E. jejuensis is characterized by small and light to dark brown crustose thalli of less than 1 cm diameter, tufts of hairs arising from the basal disc, plurangia composed mostly of two separate parallel reproductive filaments terminated by 2-4 sterile cells, and sessile unangia each with a single paraphysis. E. koreana is distinguished by olive or yellowish-brown crustose thalli of up to 3 cm diameter, tufts of hairs arising from the basal disc, and apical parts of erect filaments, plurangia with 2-5 separate reproductive filaments terminated by 2-8 sterile cells, and sessile unangia with 1-2 paraphyses. Our studies also show that "E. aurea" specimens from Japan may be recognized to be a different species from other Endoplura species.