• Parasites, Hosts and Diseases
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• v.42 no.3
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• pp.129-135
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• 2004

We compared the DNA sequences of the genus Metagonimus: M. yokogawai, M. takahashii, and M. miyatai. We obtained 288 D1 ribosomal DNA (rDNA) and mitochondrial cytochrome c oxidase subunit I (mtCOI) fragments from the adult worms by PCR, that were cloned and sequenced. Phylogenetic relationships inferred from the nucleotide sequences of the 28S D1 rDNA and mtCOI gene. M. takahashii and M. yokogawai are placed in the same clade supported by DNA sequence and phylogenie tree analysis in 28S D1 rDNA and mtCOI gene region. The above findings tell us that M. takahashii is closer to M. yokogawai than to M. miyatai genetically. This phylogenetic data also support the nomination of M. miyatai as a separate species.

• Animal Systematics, Evolution and Diversity
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• v.36 no.3
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• pp.228-231
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• 2020

Pseudohelice subquadrata (Dana, 1851) is endangered due to its restricted habitat; hence, it has been designated as a marine protected species and endangered species by law in Korea. It has been recorded only Jeju-do and Geomun-do, Republic of Korea. The present study, is the first report on a cytochrome c oxidase subunit I DNA barcode for P. subquadrata. The maximum intra-specific genetic distance among all P. subquadrata individuals was found to be 0.5%, whereas inter-genetic distance within the same genus was 17.2-21.5% compared with Helice tientsinensis (Rathbun, 1931), H. tridens (De Haan, 1835), H. epicure (Ng et al., 2018), and Helicana wuana (Rathbun, 1931). Our barcoding data can thus be used as reference for restoration and conservation studies on P. subquadrata, which are designated as marine protected species.

• Fisheries and Aquatic Sciences
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• v.26 no.11
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• pp.678-688
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• 2023

Flatfish are one of the largest families in the order Pleuronectiformes and are economically important edible marine fish species. However, they have similar morphological characteristics leading to challenges in classifying correctly, which may result in mislabeling and illegal sales, such as fraudulent labeling of processed food. Therefore, accurate identification is important to ensure the quality and safety of domestic markets in Korea. Species-specific primers were prepared from the mainly consumed eleven species of the order Pleuronectiformes. To rapidly identify the 11 flatfish species, a highly efficient, rapid, multiplex polymerase chain reaction (PCR) with species-specific primers was developed. Species-specific primer sets were designed for the mitochondrial DNA cytochrome c oxidase subunit I gene. Species-specific multiplex PCR (MSS-PCR) either specifically amplified a PCR product of a unique size or failed. This MSS-PCR analysis is easy to perform and yields reliable results in less time than the previous Sanger sequencing methods. This technique could be a powerful tool for the identification of the 11 species b the family Pleuronectidae and can contribute to the prevention of falsified labeling and protection of consumer rights.

• The Sea:JOURNAL OF THE KOREAN SOCIETY OF OCEANOGRAPHY
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• v.5 no.2
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• pp.157-168
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• 2000

Sea urchin S. intermedius occurring in the Korean east coast is a cold water species that belongs to the family Strongylocentrotidae of Echinoidea. Although it is known that there are nine species in the family, species identification criteria, phylogenetic relationships, time and process of evolution of the family members have not been uncovered clearly. In the present study, I tried to find some clues to such problems for S. intermedius by means of DNA sequences. For this, cytochrome c oxidase subunit I (COI), one of the mitochondrial genes that evolve fast and follow maternal inheritance was analyzed. DNA was extracted from the female gonad of S. intermedius, a segment of COI gene amplified by polymerase chain reaction (PCR), and finally a total of 1077 base pair sequence of COI obtained by cloning and sequencing the PCR product. The sequence was compared with homologous genes of other sea urchins and echinoderm species. Phylogenetic trees of the COI gene segment revealed that S. intenedius is a sister species of S. purpuratus which lives along the east coast of the Paciflc. With reference to the fossil records of sea urchins and genetic distances in the molecular phylogenies, it is estimated that the two species were separated about 0.89 million years ago when the earth temperature fluctuated significantly. The current disjunct distribution patterns of the two species and the climate change of the earth at the time of separation suggest that speciation might have occurred by vicariance. The COI gene sequence obtained here now can be used as a molecular character which discerns S. intermedius from the other sea urchin species of Strongylocentrotidae.

• Fisheries and Aquatic Sciences
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• v.25 no.12
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• pp.637-647
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• 2022

A spotted scat, Scatophagus argus, has a high nutritional value and is among Asia's most widely consumed fish species. Thua Thien Hue's consumption market considers this species to be of high economic value and requires protection and conservation of the population. However, the studies on the identification and genetic diversity of S. argus distributed in Vietnam are still lacking. Therefore, mitochondrial cytochrome c oxidase subunit I (COI) gene was utilized to distinguish different populations and investigate the genetic diversity of two populations of S. argus from Tam Giang lagoon, Thua Thien Hue province (n = 31) and Ca Mau province (n = 14). The sequencing results indicated 13 distinct haplotypes among 45 sequences. Five single nucleotide polymorphisms were observed to distinguish Hue spotted scat population. The S. argus population in Ca Mau province was higher haplotype diversity (Hd) and nucleotide diversity (π) than those of Thua Thien Hue province, which demonstrates that there are minor differences between haplotypes. There were genetic distances ranging from 0%-4% within the populations and 6.67% between the two populations. In addition to the sequencing, the comparison of morphology, biology, culture, and the growth rate was sufficient to distinguish the spotted scat S. argus in Thua Thien Hue from Ca Mau.

• Animal Systematics, Evolution and Diversity
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• v.28 no.3
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• pp.178-184
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• 2012

Echinoids were collected at depths of 5-10 m in Munseom, Jeju Island by SCUBA diving on November 23, 2008 and September 15, 2009. Two specimens were identified as Echinometra mathaei (Blainville, 1825) based on morphological characteristics and molecular analyses of mitochondrial cytochrome c oxidase subunit I partial sequences. Echinometra mathaei collected from Korea was redescribed with photographs and was compared with other species from GenBank based on molecular data. Phylogenetic analyses showed that no significant differences were between base sequences of E. mathaei from Korea and that from GenBank. To date, 13 echinoids including this species have been reported from Jeju Island, and 32 echinoids have been recorded in Korea.

• 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 Species Research
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• v.8 no.2
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• pp.215-224
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• 2019

We describe three feather mites recovered from a wood sandpiper Tringa glareola that was stored in a $-20^{\circ}C$ freezer at the Chungnam Wild Animal Rescue Center. These feather mites are reported for the first time in South Korea: Avenzoaria totani (Canestrini, 1978), Ingrassia veligera Oudemans, 1904 and Montchadskiana glareolae Dabert and Ehrnsberger, 1999. In this study, we provide morphological diagnoses and illustrations. Additionally, we provide partial sequences of the mitochondrial cytochrome c oxidase subunit I(COI) gene as molecular characteristics of three species.

• Journal of Mushroom
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• v.11 no.4
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• pp.201-207
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• 2013

Fungus gnats are usually found in mushroom farm and have recently become important pest because they can cause severe damage and reduce the production on shiitake mushroom. Usually shiitake mushrooms are cultivated on both oak bed logs and in the artificial sawdust beds in greenhouses. Using yellow sticky trap, the dipteran species in shiitake mushroom farm were collected from May to September in Kyonggi-do and Chungcheong-do in 2013. To identify the main species of fungus gnat on the shiitake farm in Korea, the collected samples were determined the sequence of cytochrome c oxidase subunit I (COI) by DNA barcoding. The phylogeny based on maximum likelihood analyses from COI sequence showed that Bradysia difformis and B. alpicola were main species of shiitake bed log and Scatopsidae sp. and B. difformis were dominant species of sawdust beds.

• Korean Journal of Ecology and Environment
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• v.54 no.3
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• pp.229-239
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• 2021

Thamnaconus modestus, distributed in the Northwest Pacific, has high economic value and is used in various seafood. In this study, the morphological and genetic characteristics of T. modestus and T. septentrionalis were compared and analyzed. We observed the external and internal morphology of T. modestus, sketched skeletal elements, and analyzed phylogenetic evolutionary relationships using the cytochrome c oxidase subunit I (COI) gene on mitochondrial DNA compared to T. septentrionalis. The T. modestus observed in this study had blackish-brown patterns irregularly scattered on the gray-brown body, and the fins were blue-green. Genetic analysis results based on the COI sequences of T. modestus showed seven types of base sequence variation; however, the homology was more than 98.8%. In addition, as a result of comparison of the COI nucleotide sequences and phylogenetic analysis in Tetraodontiformes, two T. septentrionalis sequences (JN813099, MW485059) were similar to T. modestus with 99% homology, and the other two T. septentrionalis sequences (EF607583, KP267619) were similar to those of species belonging to another genus Thamnaconus with 95% homology with T. modestus. It was not easy to classify the species based on morphological characteristics, and phylogenetic analysis between T. modestus and T. septentrionalis confirmed the difference in classification. These results provide the external and internal morphology of T. modestus and will be used as important information for the taxonomic study of T. modestus and T. septentrionalis.