• Title, Summary, Keyword: mtCOI

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RFLP Analysis of the mtDNA COI Region in Four Abalone Species

  • Park, Choul-Ji;Kijima, Akihiro
    • Fisheries and aquatic sciences
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    • v.9 no.3
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    • pp.101-106
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    • 2006
  • The cytochrome c oxidase subunit I (COI) gene region of mitochondrial DNA (mtDNA) was examined in four abalone species to estimate its utility as a genetic marker using restriction fragment length polymorphism (RFLP) analysis. The utility was evaluated in terms of genetic divergence and relationships among Haliotis discus hannai, H. rufescens, H. rubra, and H. midae in both hemispheres of the world. There was clear genetic divergence in the mtDNA COI region between all pairs of the four species. Moreover, relationships among the abalone species were reflected in their geographical distributions and morphological characteristics. Therefore, RFLP analysis of the mtDNA COI region is a suitable genetic marker for the estimation of genetic divergence and relationships among abalone species. However, it is not effective for the evaluation of genetic differences within abalone species.

DNA Barcoding of Isaacsicalanus paucisetus (Copepoda: Calanoida: Spinocalanidae) from the Hydrothermal Vent in the North Fiji Basin, Southwestern Pacific Ocean

  • Park, Chailinn;Lee, Won-Kyung;Kim, Se-Joo;Ju, Se-Jong
    • Animal Systematics, Evolution and Diversity
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    • v.36 no.2
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    • pp.182-184
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    • 2020
  • Isaacsicalanus paucisetus Fleminger, 1983, a monotypic species of the family Spinocalanidae Vervoort, 1951, was first reported from a hydrothermal vent field in the East Pacific Rise off the mouth of the Gulf of California. The mitochondrial cytochrome oxidase I(mtCOI) DNA barcodes are considered a useful tool to assist traditional taxonomy and species discrimination in calanoid copepods. However, the mtCOI DNA barcodes of I. paucisetus have not been reported due to the species rarity and the difficulty of sampling. In this study, we firstly determined the mtCOI DNA barcodes of the I. paucisetus newly collected from a hydrothermal vent in the North Fiji Basin of the southwestern Pacific. All mtCOI DNA barcodes of I. paucisetus were identical and intraspecies variations of spinocalanid species were 0.0-3.0%. Interspecies and intergeneric variations were 13.4-25.2% and 16.7-24.1%, respectively. The DNA barcodes of I. paucisetus obtained in the present study would be helpful for understanding taxonomic relationships of widespread spinocalanid species.

A Taxonomic Study on Perinereis nuntia Species Group (Polychaeta: Nereididae) of Korea

  • Park, Tae-Seo;Kim, Won
    • Animal Systematics, Evolution and Diversity
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    • v.23 no.1
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    • pp.75-85
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    • 2007
  • A taxonomic study was carried out on the Perinereis nuntia species group of Korea by using morphological and molecular data (mitochondrial cytochrome c oxidase subunit I: mtCOI). Two species, P. mictodonta (Marenzeller, 1879) and P. wilsoni (Glasby and Hsieh, 2006), are recognized and redescribed. In this study, mtCOI gene showed a good resolution as molecular marker for species identification of the P. nuntia species group of Korea.

Phylogenetic relationship of ribosomal ITS2 and mitochondrial COI among diploid and triploid Paragonimus westermani isolates

  • Park, Gab-Man;Im, Kyung-Il;Yong, Tai-Soon
    • The Korean Journal of Parasitology
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    • v.41 no.1
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    • pp.47-55
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    • 2003
  • We compared patterns of intraspecific polymorphism of two markers with contrasting modes of evolution, nuclear ribosomal DNA (rDNA) and mitochondrial DNA (mtDNA), in the lung fluke, diploid and triploid Paragonimus westermani from three geographical regions of Korea. The genetic distances between three populations of Korean diploid and triploid P. westermani showed no significant difference in the nucleotide sequences of the mitochondrial cytochrome c oxidase subunit 1 (mtCOI) and ribosomaal second internal transcribed spacer (ITS2) genes. A highly resolved strict-consensus tree was obtained that illustrated phylogenetically useful information of the ITS2 and mtCOI sequences from diploid and triploid P. westermani.

Sequence comparisons of 28S ribosomal DNA and mitochondrial cytochrome c oxidase subunit I of Metagonimus yokogawai, M. takahashii and M. miyatai

  • Lee, Soo-Ung;Huh, Sun;Sohn, Woon-Mok;Chai, Jong-Yil
    • The Korean Journal of Parasitology
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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.

A PCR Method to Distinguish Matsumuraeses phaseoli from M. falcana Based on the Difference of Nucleotide Sequence in the Mitochondrial Cytochrome c Oxidase Subunit I (미토콘드리아 COI 영역의 뉴클레오티드 서열 차이를 이용한 팥나방과 어리팥나방의 PCR 판별법)

  • Seo, Bo Yoon;Jung, Jin Kyo;Cho, Jum Rae;Kim, Yonggyun;Park, Chang Gyu
    • Korean journal of applied entomology
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    • v.51 no.4
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    • pp.365-370
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    • 2012
  • The two closely related major leguminous crop pests in Korea, Matsumuraeses phaseoli and M. falcana (Lepidoptera: Tortricidae) have very similar morphological characters, which occasionally give rise to a failure in distinguishing between the two. In this study, we report an easy PCR-SSP method to distinguish between them, with a sequence specific primer set (P-SF2, F-SF3, and C-SR3) based on single nucleotide mismatch in 3' terminal base of a primer, which is found in the mitochondrial cytochrome c oxidase subunit I DNA (mtCOI). Through application of this method, each species may be clearly identified in terms of its PCR band size and pattern, only one band (245 bp) for M. falcana and one (409 bp) or two bands (409 bp & 245 bp) for M. phaseoli.

A Phylogenetic Study in Some Long-Horned Beetles (Coleoptera: Cerambycidae) Using Mitochondrial COI Gene and 16S rRNA Sequences

  • Yoon, Hyung-Joo;Bae, Jin-Sik;Kim, Iksoo;Jin, Byung-Rae;Mah, Young-Il;Moon, Jae-Yu;Sohn, Hung-Dae
    • International Journal of Industrial Entomology
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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.

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Genetic Structure and Phylogenetic Relationship of Red Spotted Grouper (Epinephelus akaara) Based on the Haplotypes and Polymorphisms of Mitochondrial COI Gene Sequences (미토콘드리아 COI 유전자 서열의 다형성과 반수체형에 근거한 한국산 붉바리(Epinephelus akaara)의 유전적 구조와 계통 유연관계)

  • Han, Sang-Hyun;Lee, Young-Don;Baek, Hae-Ja;Oh, Hong-Shik;Noh, Choong Hwan
    • Journal of Life Science
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    • v.24 no.6
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    • pp.626-632
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    • 2014
  • The genetic structure and phylogenetic relationship were investigated in Korean red spotted grouper populations using the nucleotide sequence polymorphisms of the mitochondrial DNA (mtDNA) cytochrome c oxidase subunit I (COI) gene. The COI gene was sequenced showed 99.1-99.8% identity with the EF607565 sequence previously reported. A total of twenty haplotypes were found, and the Korean population showed nineteen haplotypes. Among those, Hap_03 and Hap_08 showed Jeju-do and China-specific COI sequences, respectively. However, Hap_07 had twelve COI sequences from South Korea and records from Hong Kong and Taiwan. Neighbor-joining (NJ) trees constructed from the phylogenetic analyses based on the polymorphisms of the COI haplotypes showed a monophyletic branching pattern within the genus Epinephelus. This indicated that the red spotted grouper populations had evolved from common maternal ancestors. In addition, the Hap_08, which had the COI sequence recorded only from China Sea, was found in the middle of the NJ tree nearby Hap_07 and showed a close relationship with Hap_07. This indicates that Chinese red spotted grouper is also maternally related to other populations in East Asia. Consequently, East Asian red spotted grouper populations are maternally related, as well as sharing the same evolutionary history, and are still affected by the East Asian ocean current (Kuroshio). These findings help to explain the genetic structure and phylogenetic relationship of red spotted grouper and also contribute to research on artificial breeding and industrialization.

Molecular Phylogeny and Taxonomic Review of the Family Liparidae (Scorpaenoidei) from Korea (한국산 꼼치과 어류의 분자계통 및 분류학적 재검토)

  • Song, Young Sun;Ban, Tae-woo;Kim, Jin-Koo
    • Korean Journal of Ichthyology
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    • v.27 no.3
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    • pp.165-182
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    • 2015
  • The snailfishes (Scorpaenoidei: Liparidae) is a large group requiring taxonomic reviews because of a potential taxonomic confusion due to its great similarity in external morphology between species and a variation of its body color with size. Molecular phylogeny and taxonomic review were conducted for 10 species in 3 genera reported around the Korean waters, which facilitate understanding interrelationship within its family, and further management of fisheries resources. Molecular phylogeny using mitochondrial COI (mtCOI) and nuclear RAG2 (nRAG2) sequences indicates that the reciprocal monophyly of the three genera (Careproctus, Crystallichthys, and Liparis) were supported except Crystallichthys matsushimae, being closely related to Careproctus notosaikaiensis in only mtDNA COI topology. Liparis ingens Gilbert and Burke (1912) was reported as a distinct species differing from L. ochotensis. However, in the present study, comparing L. ingens from Korea with L. ochotensis from Japan and Russia, the two species were well corresponded in their morphology and molecule, therefore, we suggest L. ingens to be treated as a junior synonym of L. ochotensis.

Comparative Study of DNA Extraction Method in Meiofauna (중형저서동물에서 효율적인 DNA 추출 방법 비교 연구)

  • Lee, Seung-Han;Back, Jin-Wook;Lee, Won-Choel
    • Korean Journal of Environmental Biology
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    • v.29 no.3
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    • pp.138-143
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    • 2011
  • The efficiency of mtCOI amplication after DNA extraction of benthic harpacticoid Tigriopus japonicus s.l. was tested under different conditions depending on fixative (99% Ethanol, or 4% Formalin) and additional chemicals (Ludox or Rose Bengal). Each experimental group by the fixative was subdivided into four groups, respectively: 1) Control (fixative only), 2) processed with Ludox HS40, 3) processed with Rose Bengal, and 4) processed with both Ludox HS40 and Rose Bengal. For the 99% ethanol-fixed sample, overall success rate of amplification by PCR was 96% or above, while for the 4% formalin-fixed one, success rate was much lower than those of ethanol-fixed: 1) Control: 27%, 2) Ludox HS40: 3%, 3) Rose Bengal: 7%, and 4) Ludox HS40 and Rose Bengal: 3%. As a result present study verify that 99% ethanol is a proper fixative for DNA extraction in meiofauna organisms.