• Korean Journal of Fisheries and Aquatic Sciences
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• v.48 no.5
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• pp.731-738
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• 2015

Nematode infection in the epithelial tissue of cultured rockfish Sebastes schlegeli was first reported in 2012. Since then, nematode infections have caused serious economic losses in rockfish aquaculture on the west coast of Korea. Taxonomic and life cycle information for this parasite are currently unknown. In this study, 18S rRNA and cytochrome c oxidase subunit I (COI) genes were used for molecular identification and polymerase chain reaction (PCR) to detect the invisible stages of this parasite. Nucleotide sequences of the 18S rRNA of the rockfish nematode showed 98% identity with that of Philometra morii. Therefore, this rockfish nematode was classified to the Philometridae family. However, we could not identify it to genus level using 18S rRNA. Its COI nucleotide sequences shared 85% and 82% identities with those of Bursaphelenchus sinensis and Philometra overstreeti, respectively. In addition, two gene-specific primer sets were designed based on the 18S rRNA gene to detect the intermediate host and nematode larvae. These primers were specific to this rockfish nematode without cross-reacting to other pathogens. The detection limit of the PCR assay using these primers was 1,000 copies of nematoda plasmid DNA. Therefore, the PCR assay described here is suitable for the detection of nematode DNA within rockfish. In addition, this PCR assay could be used to detect nematode larvae and the intermediate host.

• International Journal of Industrial Entomology and Biomaterials
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• v.2 no.1
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• pp.37-53
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• 2001

Two regions of mtDNA genome, cytochrome oxidase subunit I (COI) and 165 ribosomal RNA (165 rRNA) genes, were sequenced for 15 species of the long-horned beetle belonging to four subfamilies and geographic samples of mulberry longicorn beetle, Apriona germari, from two localities in Korea. Ten samples of A. germari collected from Suwon and Busan revealed three COI haplotypes ranging in nucleotide divergence of 0.3% to 0.5%, and the two populations shared one common COI haplotype (80%). The sequence divergence among 15 species of the long-horned beetle was much higher in COI gene (12.3%∼39.4%) than 16S rRNA gene (7.2% to 23.1), and the maximum value in the COI gene is exceptional compared with other relevant studies, including that of Coleoptera. The greatly increased divergence in the COI gene, in facto was stemmed from a peculiar sequence of Prionus insularis belonging to Prioninne, divergence of which ranges from 31.2% to 39.3% from other species. We discussed possible reason of the divergence in this species. Due to the abnormality of COI gene divergence, decrease in phylogenetic signal was severe in COI nucleotide and, subsequently, the converted amino acid sequences, rendering us to put more confidence on the 16S5 rRNA gene data. Although the molecular phylogeny confidently supports the monophyletic origin of Lepturinae, the presence of discrepancy between molecular data and traditional taxonomic views also is a testable hyothesis. One such discrepancy includes taxonomic position of Sophronica obrioides and Theophilea cylindricollis belonging to Lamiinae.

• Journal of Apiculture
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• v.32 no.2
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• pp.119-131
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• 2017

For the Rapid detection of small hive beetle (SHB; Aethina tumida) and for the mass-survey against SHB invasion, SHB-specific ultra-rapid PCR system was developed. Three different pairs of Aethina tumida-specific primers were deduced from cytochrome oxidase subunit I (COI) gene in mitochondrial DNA of SHB. Using optimized SHB-specific ultra-rapid PCR, $2.1{\times}10^1$ molecules of COI gene belonged to SHB could be detected specifically and quantitatively within 18 minutes 40 seconds. For the purpose of the application in apiary field, a DNA extraction method from bee debris was separatedly developed. When $10^5$ SHB-specific COI molecules (1/1000 body of SHB larvae) are existed in 1g of bee debris, it could be verified inner 10 minutes as qualitative and quantitative manner. SHB-specific ultra-rapid PCR we proposed would be expected to apply widely, either in apiary field or laboratory, for the rapid detections and the control against SHB-invasion.

• Journal of fish pathology
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• v.36 no.2
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• pp.403-408
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• 2023

Mullet is an important marine aquaculture fish species in Korea, with a total of 7,237 tons produced as of 2022, making it the 5th most produced marine aquaculture fish species. In this study, ectoparasites presumed to be isopods were discovered in the fins of farmed flathead grey mullet (average weight 550 g), and the characteristics of the parasites were confirmed. The length of the parasite was 5 to 18 mm, and 3 to 7 parasites were infected per fish. To analyze the characteristics of the parasites, molecular biological identification and phylogenetic analysis were performed using the cytochrome c oxidase subunit I (COI) gene, and it was confirmed to be most closely related to Nerocila japonica in the Cymothoidae family. To confirm the parasite control effect, a direct exposure drug sensitivity test was conducted on five types of aquatic drugs and fresh water, trichlorfon was confirmed to be effective.

• Animal Systematics, Evolution and Diversity
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• v.36 no.3
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• pp.258-263
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• 2020

The aim of this study is to report monotypic species, Nonparahalosydna pleiolepis(Marenzeller, 1879) for the first time from Korean waters with its DNA barcoding data. We collected individuals of the species from the subtidal zone of southern coast of Korea through scuba diving. To estimate DNA barcoding gap, the pairwise genetic distances were calculated between N. pleiolepis and its congeners (Halosydna brevisetosa Kinberg, 1856 and Lepidonotus squamatus (Linnaeus, 1758)) based on the cytochrome c oxidase subunit I gene (COI). Inter-specific genetic distances ranged from 18.7% to 24.6%, while intra-specific genetic distance within N. pleiolepis ranged from 0.3% to 0.5%. The maximum intra-specific genetic distance among the three species was 1.4%. The morphological diagnosis of N. pleiolepis with a taxonomic note on the species were also provided.

• Animal Systematics, Evolution and Diversity
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• v.35 no.2
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• pp.84-90
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• 2019

The brittle star, Amphistigma minuta H.L. Clark, 1938, was collected from Munseom Island, Jeju-do, Korea, by SCUBA diving. This species has distinct morphological features, as follows: a small disk with large papillae on the disk margin; slender arms and four arm spines at proximal; and oral parts the same as those of the genus Amphipholis. Additionally, we obtained partial sequences of the cytochrome c oxidase subunit I gene (COI) (513 bp) and compared them with sequences from Australian A. minuta and 13 other species of Amphiuridae. As a result, intraspecific pairwise distance was 0.4% between two Korean individuals and intraspecific distance between the Australian and the Korean populations was 2.6-2.8%, which indicates they should be considered as the same species. Ultimately, 15 species of the family Amphiuridae have currently been recorded in Korea, including A. minuta.

• Animal Systematics, Evolution and Diversity
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• v.36 no.4
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• pp.396-399
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• 2020

The Antarctic freshwater copepod, Boeckella poppei (Mrazek, 1901), has the widest range of distribution extending from southern South America to Antarctic continent, among all Boeckella species. Boeckella poppei is the only freshwater copepod known to be inhabiting the Antarctic continent. In present study, we analyzed the DNA barcodes of the mitochondrial cytochrome c oxidase subunit I (COI) gene of B. poppei from King George Island, Antarctica. The intraspecific genetic distances varied from 0% to 13% and interspecific genetic distances ranged from 11% to 14%. The overlap of DNA barcode gap suggests careful threshold-based delimitation of species boundaries.

• Animal Systematics, Evolution and Diversity
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• v.39 no.4
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• pp.295-299
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• 2023

Two land snails, Aegista chejuensis (Pilsbry and Hirase, 1908) and Plectotropis quelpartensis (Pilsbry and Hirase, 1908), are endemic to Korea and were collected from Hataedo and Jodo Islands in the Yellow Sea of South Korea, respectively. Many terrestrial snail habitats have been confirmed in Korea; however, their genetic sequences have rarely been reported. This study describes the mitochondrial cytochrome c oxidase subunit I gene (COI) sequences of two species, followed by an analysis of the genetic distance between these two species and their congeners. As a result, there was no intra-species variation in both species A. chejuensis or P. quelpartensis. However, the inter-species variation was clear (10.3-31.5%). We provide photographs and a brief diagnosis for morphological verification.

• 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.

• Korean Journal of Environment and Ecology
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• v.28 no.5
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• pp.523-530
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• 2014

One juvenile raptor which was not able to be identified due to its head damage was discovered on a roadside in Janggok-ri, Jori-eup, Paju on 28th June, 2011. The species was identified by DNA barcoding. After polymerase chain reaction (PCR) of the mitochondrial cytochrome c oxidase subunit I gene (COI), we obtained 695 bp sequences. We analyzed the obtained COI sequence with similar sequences from the BOLD systems and BLAST of the NCBI Genbank, and discovered that its sequence showed 100 % similarity values with the one of the five gray-faced buzzards which were previously researched. In addition, it was confirmed to be a female through sex determination using DNA. Such results are important information as it confirms the breeding of the gray-faced buzzards for the first time in 43 years since its breeding was last recorded in 1968, in Paju. Wildlife rescue center needs to work with adjacent consigned registration and preservation institutions when carcass of wild animals is collected or DNA samples are obtained for more accurate both species and sex identification through a systematic management system in the future. Furthermore, the obtained DNA sample of the gray-faced buzzard and COI gene, DNA barcode, could be used as reference standards for similar researches in the future.