• Journal of Life Science
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• v.21 no.7
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• pp.939-946
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• 2011

Sequence data of Cytochrome Oxidase Subunit I (COI) gene of mitochondria were used to elucidate the taxonomy and phylogenetic relationships of the terrestrial planarian taxa in Korea. Published COI gene sequences from Family Bipaliidae in GenBank were also included in the phylogenetic analysis. The aligned data sets for Terricola ranged from 387 to 444 nucleotides (bp) as a result of differences in insert nucleotides. The phylogeny based on COI analysis was not congruenced with the morphological traits. Bipalium nobile included the remainder taxa (Bipalium adventitium, Bipalium venosum, Bipalium kewense, and Bipalium multilineatum). Internal nodes were strongly supported (>91%). The phylogenetic tree on COI analysis showed that most identified species were well separated from each other. The main phylogenetic analysis formed monophyletic groups. COI gene of mitochondria could have the resolving power for taxonomy information for the terrestrial planarian taxa in Korea.

• Journal of information and communication convergence engineering
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• v.21 no.2
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• pp.159-166
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• 2023

The COI gene is a sequence of approximately 650 bp at the 5' terminal of the mitochondrial Cytochrome c Oxidase subunit I (COI) gene. As an effective DeoxyriboNucleic Acid (DNA) barcode, it is widely used for the taxonomic identification and evolutionary analysis of species. We created a CNN-LSTM hybrid model by combining the gene features partially extracted by the Long Short-Term Memory ( LSTM ) network with the feature maps obtained by the CNN. Compared to K-Means Clustering, Support Vector Machines (SVM), and a single CNN classification model, after training 278 samples in a training set that included 15 genera from two orders, the CNN-LSTM hybrid model achieved 94% accuracy in the test set, which contained 118 samples. We augmented the training set samples and four genera into four orders, and the classification accuracy of the test set reached 100%. This study also proposes calculating the cosine similarity between the training and test sets to initially assess the reliability of the predicted results and discover new species.

• Animal cells and systems
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• v.15 no.3
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• pp.243-249
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• 2011

The genetic diversity and population history of the Asian shore crab, Hemigrapsus sanguineus, were investigated with a nucleotide sequence analysis of 536 base pairs (bp) of the mitochondrial cytochrome c oxidase subunit I gene (COI) in 111 samples collected from four populations in Korea and one in Japan. In total, 28 haplotypes were defined by 27 variable nucleotide sites in the COI region examined. The observed haplotypes had a shallow haplotype genealogy and no geographical associations. Most of the populations had high haplotype diversity (0.656-0.788) and low nucleotide diversity (0.00165-0.00244), and significant negative values for Fu's $F_S$, suggesting rapid and recent population growth from an ancestral population and sudden population expansion. The pairwise fixation indices ($F_{ST}$) estimated with the exact test and the migration rates indicate that substantial gene flow occurs among these populations as a result of sea currents, except between the Yellow Sea coast of Korea (BUA) and the Pacific Ocean coast of Japan (JPA). These two populations (BUA and JPA) showed significant genetic differentiation and low migration rate.

• Parasites, Hosts and Diseases
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• v.45 no.3
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• pp.181-190
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• 2007

The phylogenie relationships existing among 14 parasitic Platyhelminthes in the Republic of Korea were investigated via the use of the partial 28S ribosomal DNA (rDNA) D1 region and the partial mitochondrial cytochrome c oxidase subunit 1 (mCOI) DNA sequences. The nucleotide sequences were analyzed by length, G + C %, nucleotide differences and gaps in order to determine the analyzed phylogenie relationships. The phylogenie patterns of the 28S rDNA D1 and mCOI regions were closely related within the same class and order as analyzed by the PAUP 4.0 program, with the exception of a few species. These findings indicate that the 28S rDNA gene sequence is more highly conserved than are the mCOI gene sequences. The 28S rDNA gene may prove useful in studies of the systematics and population genetic structures of parasitic Platyhelminthes.

• 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.

• 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.16 no.4
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• pp.243-251
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• 2013

Genetic diversity and gene flow patterns in Pollicipes mitella were investigated with a nucleotide sequence analysis of 514 base pairs from the mitochondrial cytochrome c oxidase subunit I gene (COI) in 124 samples collected from six Korean populations. In total, 59 haplotypes were defined by 40 variable nucleotide sites in the COI region. The haplotypes had shallow haplotype genealogy and no geographic associations. All populations had high haplotype diversity (0.909 to 0.979) and low nucleotide diversity (0.0055 to 0.0098). The haplotypes with recently diverged nucleotides were distributed by long-range larvae dispersal among regional populations. The pairwise fixation indices ($F_{ST}$) estimated with the exact test and migration rates indicate that substantial gene flow has occurred among populations as a result of sea currents, except between the Uljin (East Sea coast) and other Korean populations. This suggests that significant genetic differentiation and low migration rates have affected the Uljin population.

• Journal of Life Science
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• v.26 no.4
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• pp.406-413
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• 2016

Abalones are gastropod mollusks belonging to the genus Haliotis. Pacific abalones are regarded as a very important marine gastropod mollusk in Korea, Japan, China, and also in food industries around the world. In Korea, 6 species of abalone have been reported to occur along the coasts: Haliotis discus hannai, Haliotis discus discus, Haliotis madaka, Haliotis gigantea, Haliotis diversicolor supertexta, and Haliotis diversicolor diversicolor. This study was performed to discriminate the genetic variances by the partial sequences of the mitochondrial cytochrome c oxidase subunit I (COI) genes and random amplified polymorphic DNA (RAPD) analysis against four species of Pacific abalone (H. discus hannai, H. discus, H. madaka, H. gigantea). COI gene is reasonably well conserved and has been sequenced in various invertebrate taxa. The RAPD analysis technique is a relatively simple and low cost method that allows differentiation of taxa without the need to know their genomes. In this study, we investigated the genetic diversity, phylogenetic relationships within each species. The COI and RAPD analysis were able to distinguish between H. gigantea and the other three species. However, these analysis methods were inadequate to distinguish between H. discus and H. madaka. These results are believed to be able to provide a basis data for future hybrid breeding research by defining the genetically closely related four species of abalone, which is to develop new hybrid abalone for export using hybrid breeding.

• 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.

• 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.