• Korean Journal of Ecology and Environment
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• v.55 no.3
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• pp.212-220
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• 2022

An estuary is a water ecosystem with a high abundance of the species diversity, due to a variety of complex physicochemical factors of the area where freshwater and ocean mixed. The identification of Corbicula species in the estuary environments is difficult because of various morphological characteristics. In this study, we provide taxonomic information on Corbicula species with taxonomic difficulties using morphological and genetic analysis. This study was conducted on clams from the Seomjin River-Gwangyang Bay, one of the major production area of marsh clam in Korea. As a result, we characterized Cytocrome C Oxidase subunit I (COI) sequences of the Corbicula. The 636 bp nucleotide sequences of COI have 98% homology among Corbicula species collected from 2 sites of Seomjin River-Gwangyang Bay. The phylogenetic analysis with 17 species of Corbicula indicated that most of the species collected from Seomjin River-Gwangyang Bay were brackish water clam (Corbicula japonica), and only one Asian clam (Corbicula fluminea). The evolutionary distance between C. japonica and C. fluminea was less than 0.003. Therefore, it was confirmed that C. japonica is phylogenetically closely related to C. fluminea. In 9 species of Cyrenidae, phylogenetic tree was classified into three lineages. These results will be used as an important data for an identification of clam species by providing genetic information for Corbicula species with a morphological diversity.

• Research in Plant Disease
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• v.23 no.3
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• pp.241-248
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• 2017

The purpose of this study was to develop rapid methods for distinguishing between Heterodera schachtii and H. glycines detected from chinese cabbage fields of highland in Gangwon, Korea. To do this, we performed PCR-RFLP and PCR with the primers set developed in this study for GC147, GC408 and PM001 population, H. schachtii, and YS224, DA142 and BC115 population, H. glycines. Eight restriction enzymes generated RFLP profiles of mtDNA COI region for populations of H. schachtii and H. glycines, repectively. As a result, treatment of two restriction enzymes, RsaI and HinfI, were allowed to distinguish H. schachtii from H. glycines based on the differences of DNA band patterns. The primer set, #JBS1, #JBG1 and #JB3R, amplified specific fragments with 277 and 339 bp of H. schachtii, 339 bp of H. glycines, respectively, while it did not amplify fragments from three root-knot nematodes and two root-lesion nematodes. Thus, the primer set developed in this study could be a good method, which is used to distinguish between H. schachtii and H. glycines.

• Korean Journal of Ecology and Environment
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• v.53 no.3
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• pp.286-294
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• 2020

The Chironomus(Diptera: Chironomidae) is a freshwater benthic invertebrate that is an important indicator organism used for environmental pollution and water quality monitoring. In this study, we performed morphological classification and genetic species identification using the cytochrome c oxidase subunit I (COI) gene on mitochondrial DNA for an accurate species classification of Chironomus larvae found in tap water purification plants in Incheon, Korea. Twenty larvae in six water purification plants consist of four species, including twelve Chironomus kiiensis, six Chironomus flaviplumus, one Chironomus dorsalis, and one Polypedilum yongsanensis (not included Genus Chironomus). Morphological characteristics of each larvae were identified based on the head capsule, the mentum, the mandible, the antenna, and the claw. Based on the COI sequences of 21 individuals of 17 Chironomus species registered in NCBI Genbank, phylogenetic analysis indicated that the 20 individuals investigated in this study consist of the same clade with corresponding species of the high homology (99~100%) including C. kiiensis, C. flaviplumus, C. dorsalis, and P. yongsanensis. These results will be used as main classification indicator for monitoring freshwater ecosystems by providing integrated morphological and genetic information for the species identification of Korean Chironomus.

• Korean Journal of Ecology and Environment
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• v.52 no.3
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• pp.221-230
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• 2019

Barbel steed (Hemibarbus labeo) is a small freshwater fish species as semi-bottom dwellers distributed in eastern Asia. We carried out characterization of the cytochrome c oxidase subunit I (COI) gene from the mitochondrial DNA of H. labeo in the Sumjin River to identify the phylogenetic location of H. labeo in the genus Hemibarbus and Cyprinidae. Multiple alignment of the 577 bp COI sequence revealed high sequence homology (99~100%) between Seomjin River H. labeo. The nucleotide sequence similarity between H. labeo (HD1) and H. mylodon was 88.91% and that of H. longirostis was 88.81% among the three species found in Korea. In addition, the nucleotide sequence similarities of H. maculatus, H. meditus, H. umbrifer and H. barbus showed 98.97%, 97.20%, 96.87% and 98.85%, respectively. Phylogenetic analysis on seven species of the genus Hemibarbus showed that the H. labeo collected in this study formed two clades. One of which consisted of Hadong, Imsil, Kangjin. The other one formed a step with HD2, HD8 and HD9 of Hadong and the H. labeo reported in Busan, Asan and Seoul, Korea. Phylogenetic position of the H. labeo among Cyprinidae showed 0.143 for the evolutionary distance from Zacco platypus and 0.006 for the H. maculatus. In addition, the genetic position of the H. labeo among 28 species of Cyprinidae was found to be located in Group I, including Gobioninae fishes. The results of this study will provide key genetic information for the taxonomic comparison in Cyprinidae and study of model fish for pollution monitoring in freshwater environments.

• Journal of Sericultural and Entomological Science
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• v.51 no.2
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• pp.201-206
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• 2013

Aporia crataegi, an Korean endangered species, was first analyzed for DNA barcode sequences based on 28-year-old dried specimens and compared barcode characters with 36 individuals of ten geographical populations of Eurasia. They were revealed to consist of five different haplotypes. Among them, haplotype I was mostly extensive and high frequency with 75%. The south Korean individuals were confirmed to be belonging to haplotype I and have no genetic isolation on COI gene. By these results, we consider that selection of the identical haplotype from other geographical populations may be a requirement prior to performing for conservation and restoration of the Korean population. We also propose to analyse the additional genetic markers in order to understand a more accurate genetic structures between haplotypes of this species.

• 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 applied entomology
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• v.59 no.1
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• pp.73-78
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• 2020

The fall armyworm, Spodoptera frugiperda (Smith, 1797), originated from tropical and subtropical America is one of sporadic agricultural pests in the world. Since the moth has high migration capacity, it rapidly expanded the world distribution such as Africa in 2016, India in 2018, and East-Asian countries in 2019. In Korea, this species was firstly found at maize fields of Jeju Island, in early June 2019, and subsequently detected at many counties of Jeolla-do and Gyeongsang-do in June and July 2019. The first invaded populations of S. frugiperda in Korea were genetically confirmed as one species, S. frugiperda by using a mitochondrial cytochrome oxidase subunit I (COI) gene, and analyzed to be comprised of two haplotypes (hap-1 and hap-2) each belonging to different clades. Among 31 COI sequences, the hap-1 sequence was predominant, accounting for 93.5%.

• Journal of Life Science
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• v.31 no.1
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• pp.66-72
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• 2021

This study developed a species identification method for the salted opossum shrimp of Acetes japonicus, A. chinensis (Korea, China), A. indicus (I, II), and Palaemon gravieri based on PCR-RFLP markers. Genomic DNA was extracted from the salted opossum shrimp. The COI gene was used to amplify 519 base pairs (bp) using specific primers. The amplified products were digested by Acc I and Hinf I, and the DNA fragments were separated by automated electrophoresis for RFLP analysis. When the amplified DNA product (519 bp) was digested with Acc I, A. japonicus, A. chinensis (Korea), and A. indius (II) showed two fragments, whereas a single band of 519 bp was detected in A. chinensis (China) and A. indius (I). Also, in the RFLP patterns digested by Hinf I, A. chinensis (Korea) and A. chinensis (China) showed a single band of 519 bp, while two fragments were observed in A. japonicus and A. indius (I) and four fragments in A. indius (II). The PCR amplicon of P. gravieri was digested by Acc I into 3 bands of 271, 202, and 46 bp and by Hinf I into a single band of 519 bp. Therefore, salted opossum shrimp-specific RFLP markers showing distinct differences between four species and two sub-species by PCR-RFLP analysis. Thus, the PCR-RFLP markers developed in this study are a good method for identifying the six types of salted opossum shrimp.

• Korean Journal of Ichthyology
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• v.32 no.4
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• pp.199-209
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• 2020

In order to clarify the taxonomic status of the Korean Macroramphosus species, which were previously confused, we investigated morphological and molecular variations of Macroramphosus (18 individuals) from Korea, and Macroramphosus (35 individuals) from Japan and Taiwan, and compared with those of M. scolopax from type locality (Mediterranean Sea). Although the Korean and Japanese specimens of Macroramphosus were clearly divided into two types in the first dorsal spine length (22.8~32.1% in A-type vs. 15.6~21.4% in B-type), distance between the first dorsal fin and second dorsal fin (6.4~9.7% vs. 8.6~13.3%), and body depth (20.0~28.0% vs. 17.3~22.6%), no genetic differences among all individuals of longspine snipefish between them were found at the specific level [d=0.0~3.3% in control region (CR); 0.0~1.3% in cytochrome b (cytb); 0.0~0.5% in cytochrome c oxidase subunit I (COI)]. Whereas, they were well distinguished in genetics (9.9~11.5% in CR; 3.8~4.6% in cytb; 1.2~3.6% in COI) from those of M. scolopax in Mediterranean Sea. It needs the scientific name of the longspine snipefish (M. scolopax) in Korea be changed as M. japonicus (and/or M. sagifue). However, our results could not find evidence of consistency between morphological and mitochondrial DNA variations which suggests that their differentiation event may occur fairly recently. Further studies using more sensitive markers such as microsatellite are needed to clarify the degree of gene flow between the two types.