• 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.

• International Journal of Industrial Entomology and Biomaterials
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• v.35 no.1
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• pp.51-57
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• 2017

The tiny dragonfly, Nannophya pygmaea (Odonata: Libellulidae), is an endangered insect in South Korea. Previously, a partial mitochondrial DNA sequence that corresponded to a DNA barcoding region has been used to infer genetic diversity and gene flow. In this study, we additionally sequenced the barcoding region from N. pygmaea that had been collected from three previously sampled populations (40 individuals) and these sequences were combined with the preexisting data. We also selected and sequenced an additional mitochondrial gene (ND5) to find further variable gene regions in the mitochondrial genome. DNA barcoding sequences of 108 individuals from five South Korean localities showed that genetic diversity was highest in Gangjin, Jeollanam-do Province. Muuido, which was previously occupied by a single haplotype, was also found to have an identical haplotype, which confirmed the low genetic diversity on this islet. Gene flow among populations is highly limited, and no clear distance- or region-based geographic partitioning was observed. Phylogenetic relationships among haplotypes showed that there were no discernable haplotypes in South Korea. ND5 provided slightly more haplotypes compared to the barcoding region in 40 individuals (14 vs. 10 haplotypes in the COI gene). It also had a slightly higher within-locality diversity estimate, which suggested that ND5 had potential as mitochondrial DNA-based marker for population genetic analysis.

• Journal of Food Hygiene and Safety
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• v.33 no.4
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• pp.280-288
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• 2018

In this study, an approach for the analysis of the five cephalopod species (octopus, long-arm octopus, squid, wet-foot octopus, beka squid) consumed in the Republic of Korea is developed. The samples were collected from the Southeast Asian countries Thailand, Indonesia, Vietnam, and China. The SYBR-green-based real-time qPCR method, based on the mitochondrial DNA genome of the five cephalopods was developed and validated. The intergroup variations in the mitochondrial DNA are evident in the bioinformatic analysis of the mitochondrial genomic DNA sequences of the five groups. Some of the highly-conserved and slightly-variated regions are identified in the mitochondrial cytochrome-c-oxidase subunit I (COI) gene, 16s ribosomal RNA (16s rRNA) gene, and 12s ribosomal RNA (12s rRNA) gene of these groups. To specify each five cephalopod groups, specific primer sets were designed from the COI, 16s rRNA and 12s rRNA regions. The specific primer sets amplified the DNA using the SYBR-green-based real-time PCR system and 11 commercially secured animal tissues: Octopus vulgaris, Octopus minor, Todarodes pacificus, Dosidicus gigas, Sepia esculenta, Amphioctopus fangsiao, Amphioctopus aegina, Amphioctopus marginatus, Loliolus beka, Loligo edulis, and Loligo chinensis. The results confirmed by a conveient way to calculate relative amplification levels between different samples in that it directly uses the threshold cycles (Ct)-value range generated by the qPCR system from these samples. This genomic DNA-based molecular technique provides a quick, accurate, and reliable method for the taxonomic classification of the animal tissues using the real-time qPCR.

• Proceedings of the Korean Society of Applied Entomolohy Conference
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• 2000.05a
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• pp.101-101
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• 2000

• Molecules and Cells
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• v.28 no.4
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• pp.347-363
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• 2009

The 15,389-bp long complete mitogenome of the endangered red-spotted apollo butterfly, Parnassius bremeri (Lepidoptera: Papilionidae) was determined in this study. The start codon for the COI gene in insects has been extensively discussed, and has long remained a matter of some controversy. Herein, we propose that the CGA (arginine) sequence functions as the start codon for the COI gene in lepidopteran insects, on the basis of complete mitogenome sequences of lepidopteran insects, including P. bremeri, as well as additional sequences of the COI start region from a diverse taxonomic range of lepidopteran species (a total of 53 species from 15 families). In our extensive search for a tRNA-like structure in the A+T-rich region, one $tRNA^{Trp}$-like sequence and one $tRNA^{Leu}(UUR)$-like sequence were detected in the P. bremeri A+T-rich region, and one or more tRNA-like structures were detected in the A+T-rich region of the majority of other sequenced lepidopteran insects, thereby indicating that such features occur frequently in the lepidopteran mitogenomes. Phylogenetic analysis using the concatenated 13 amino acid sequences and nucleotide sequences of PCGs of the four macrolepidopteran superfamilies together with the Tortricoidea and Pyraloidea resulted in the successful recovery of a monophyly of Papilionoidea and a monophyly of Bombycoidea. However, the Geometroidea were unexpectedly identified as a sister group of the Bombycoidea, rather than the Papilionoidea.

• Molecules and Cells
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• v.19 no.3
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• pp.391-397
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• 2005

Molecular identification techniques are used where morphological characters are not useful for distinguishing species that resemble each other closely. The example studied here is the Adoxophyes species complex, in which A. orana (Fischer von $R{\ddot{o}}sslerstamm$) is officially the only known Korean species in the genus Adoxophyes (Lepidoptera: Tortricidae). However there have been suspicions that at least two types of A. orana exist in Korea based on the distribution and range of the host, with A. orana attacking apples and peaches, and another Adoxophyes sp. attacking tea and pears. The latter is presumed to be A. honmai (Yasuda), but the two have remained confused because of their extreme morphological similarity, despite several Asian studies of pheromonal and morphological characteristics. To confirm the occurrence of an Adoxophyes species other than A. orana in Korea, we compared 940 bp of the mitochondrial cytochrome oxidase I (COI) gene from 16 samples of Adoxophyes and found that there is a second Adoxophyes species different from A. orana. Comparison of the different sequences to that of Japanese A. honmai confirmed that they belong to the latter. From the sequence difference between the two Korean species, we were able to develop new PCR primer sets that distinguish them. This molecular identification technique with no enzyme digestion or sequencing step is a convenient and rapid way of differentiating between species that are hard to distinguish morphologically.

• International Journal of Industrial Entomology and Biomaterials
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• v.24 no.1
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• pp.41-47
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• 2012

The Scarites aterrimus (Coleoptera: Carabidae) dwells exclusively on coastal sandy dunes. Previously, we investigated the nation-wide magnitude and nature of genetic diversity of the species using mitochondrial COI gene and found moderate to low magnitude of sequence diversity, the presence of closely related haplotypes, and relatively high gene flow estimate. Based on these observations we concluded that the species had no historical barriers that bolster genetic subdivision and possible population decline. In this study, we additionally sequenced mitochondrial COII gene from 23 individuals collected from 9 Korean localities to confirm previous findings. Sequencing of 688 bp COII gene provided 5 haplotypes ranging in sequence divergence from 0.145% to 0.291% (1 ~ 2 bp), further confirming low sequence divergence of the species. Gene flow estimates and genetic diversity estimates also support the previous findings that there had been no historical barriers that bolster genetic subdivision.

• Journal of Apiculture
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• v.33 no.4
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• pp.227-237
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• 2018

The majority parasitic bee mites of Thailand in genus Tropilaelaps are infesting colonies of native bees (Apis dorsata) and introduced bees (A. mellifera). The investigation aims to study morphological and genetic variation of Tropilaelaps mites infected different hosts. Adult mites were collected from honey bee brood throughout Thailand. Traditional and geometrical morphometrics were measured on photograph by using TPS program. Additional, COI gene variations were examined by PCR-RFLP and nucleotides sequencing. Tree of mites relationships were constructed by NJ and MP assumptions. Morphometric results indicated T. mercedesae were major species infesting on A. dorsata and A. mellifera. Mophological variation represented at anal and epigynial plate, which the shape of the anal plate apex margin has been key character to identify between T. mercedesae (bell to blunt shape) and T. koenigerum (pear shape). However, the discriminant analysis suggested that geometric results were potential to classify Thai Tropilaelaps populations from different hosts better than traditional morphometric. Otherwise, PCR-RFLP clearly detected the site of Dra I and Xba I digestion of Thai Tropilaelaps morphotypes. The COI sequences of T. koenigerum were founded infesting only A. dorsata in Thailand and four sequences that related to the Thai T. mercedesae morphotypes. The NJ and MP tree were clearly classified Thai Tropilaelaps species which were suggested both from morphological and molecular analysis. This information might be basically of taxonomic status, but this should have implication for controlling these mites in Thailand and other countries.

• Animal Systematics, Evolution and Diversity
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• v.33 no.3
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• pp.169-175
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• 2017

In the northwestern Pacific region, the pen shell (Atrina pectinata) is a widely distributed bivalve and economically important in fisheries. Recently, stock of this species has been greatly reduced due to overexploitation and marine pollution, which arouses interest in conservation. Studies on genetic and taxonomic entities of pen shells have not been tried in Korea, which makes difficult to take measures for effective conservation of this marine resource. In this study, we investigated mitochondrial genetic polymorphism of pen shells collected from 4 locations in Korea and Japan using cytochrome c oxidase I (COI) gene sequences. A total of 39 haplotypes were identified among 86 individuals of pen shell. Although only 5 haplotypes were shared, no significant genetic differentiation was observed between Korean and Japanese populations. These results suggest that pen shell populations of these regions share an ancestral population which might have experienced expansion during the Pleistocene, but gene flow must have been highly restricted after expansion.

• Animal Systematics, Evolution and Diversity
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• v.28 no.1
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• pp.36-41
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• 2012

The larvae of Chaoborus are widely distributed in lakes, ponds, and reservoirs. These omnivorous Chaoborus larvae are crucial predators and play a role in structuring zooplankton communities, especially for small-sized prey. Larvae of Chaoborus are commonly known to produce predator-induced polyphenism in Daphnia sp. Nevertheless, their taxonomy and molecular phylogeny are very poorly understood. As a fundamental study for understanding the role of Chaoborus in predator-prey interactions in a freshwater ecosystem, the molecular identification and phylogenetic relationship of Chaoborus were analyzed in this study. A molecular comparison based on partial mitochondrial cytochrome oxidase I (COI) between species in Chaoborus was carried out for the identification of Chaoborus larvae collected from 2 localities in Korea. According to the results, the Chaoborus species examined here was identified as C. flavicans, which is a lake-dwelling species. Furthermore, partial mitochondrial genome including COI, COII, ATP6, ATP8, COIII, and ND3 were also newly sequenced from the species and concatenated 5 gene sequences excluding ATP8 with another 9 dipteran species were compared to examine phylogenetic relationships of C. flavicans. The results suggested that Chaoborus was more related to the Ceratopogonidae than to the Culicidae. Further analysis based on complete mitochondrial DNA sequences and nuclear gene sequences will provide a more robust validation of the phylogenetic relationships of Chaoborus within dipteran lineages.