• Title/Summary/Keyword: COI

Search Result 290, Processing Time 0.108 seconds

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
    • /
    • v.24 no.6
    • /
    • pp.626-632
    • /
    • 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.

Conflict of interest in medical research (의학연구에서의 이해충돌)

  • Kwon, Ivo
    • The Journal of KAIRB
    • /
    • v.1 no.2
    • /
    • pp.23-29
    • /
    • 2019
  • "Conflict of Interest(COI)" is defined as a situation where a person or an institution is involved in multiple interests, and an interest is against the others. COI in medical researches should well addressed and managed in order not to breach the integrity of the research. Numbers of methods have been introduced to manage the COI. In this article, the concept of COI and its application to medical researches is reviewed and the methods evading COI are introduced.

  • PDF

Phylogenetic Relationship Among Four Species of Korean Oysters Based on Mitochondrial 16S rDNA and COI Gene (미토콘드리아 16S rDNA와 COI유전자에 근거한 한국산 굴류 4종의 유연관계)

  • 이상엽;박두원;안혜숙;김상해
    • Animal Systematics, Evolution and Diversity
    • /
    • v.16 no.2
    • /
    • pp.203-211
    • /
    • 2000
  • Partial mitochondrial 16S rDNA and COI gene were amplified using PCR and sequenced for four species of oysters in Korea. Phylogenetic relationships among them were inferred from their aligned sequences by neighbor-joining method. The sequence comparison data of two mitochondrial genes showed that the genetic distinction between two oyster genera (Crassostreo and Ostrea) was obvious. Phylogenetic analysis based on the nucleotide sequences and A+T percentage of two genes indicates that C. gigas and C. nippona strongly formed a sister group and then C. ariakensis was clustered with the clade although that based on amino acid sequences of COI gene by neighbor-joining method represented different phylogenetic tree.

  • PDF

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
    • /
    • v.2 no.1
    • /
    • pp.37-53
    • /
    • 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.

  • PDF

Identification and Phylogenetic Relationship at Cytochrome Oxidase Subunit I (COI) Gene among Korean Terrestrial Planarian Taxa (한국 내 육지플라나리아 간 치토크롬 산화효소의 동정과 계통유전학적 관계)

  • Moon, Doo-Ho;Lee, Young-Ah;Huh, Man-Kyu
    • Journal of Life Science
    • /
    • v.21 no.7
    • /
    • pp.939-946
    • /
    • 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.

DNA Barcoding of Benthic Ragworms of the Genus Nectoneanthes (Polychaeta: Nereididae) Collected in Korean Waters

  • Park, Taeseo
    • Animal Systematics, Evolution and Diversity
    • /
    • v.37 no.3
    • /
    • pp.235-241
    • /
    • 2021
  • To provide better taxonomic information of the genus Nectoneanthes, the two DNA barcode regions of mitochondrial cytochrome c oxidase subunit I (COI) and 16S ribosomal DNA (rDNA) sequences of Nectoneanthes oxypoda and N. uchiwa were determined. In addition, the respective sequences of four nereidid species closely related to Nectoneanthes were retrieved from GenBank for comparison and to estimate intra- and inter-specific genetic distances. The aligned sequence lengths of COI and 16S rDNA were 570 bp and 419 bp long, respectively. The mean intraspecific variation in both markers was less than 1% in all species except for that in COI of H. diadroma (1.87%). The mean interspecific variation between N. oxypoda and N. uchiwa was 12.02% regarding COI and 1.85% regarding 16S rDNA. In contrast, the mean interspecific variation between species of other genera was comparably higher(i.e., genus Perinereis: 20.5% in COI and 8.3% in 16S rDNA; genus Hediste: 13.18% in COI and 2.64% in 16S rDNA), compared with that between the two Nectoneanthes species. This result indicated that these Nectoneanthes species are genetically more closely related than other congeneric species of different genera. The DNA barcoding information on Nectoneanthes species generated in this study provides valuable insights for further biodiversity studies on nereidid species.

Assaying Mitochondrial COI Sequences and Their Molecular Studies in Hexapoda, PART I: From 2000 to 2009 (육각강에서 보고된 미토콘드리아 COI 염기서열과 이들을 이용한 분자 연구 논문 분석, 파트 I: 2000년~2009년)

  • Lee, Wonhoon;Park, Jongsun;Akimoto, Shin-Ichi;Kim, Sora;Kim, Yang-Su;Lee, Yerim;Kim, Kwang-Ho;Lee, Si Hyeock;Lee, Yong-Hwan;Lee, Seunghwan
    • Korean journal of applied entomology
    • /
    • v.52 no.4
    • /
    • pp.395-402
    • /
    • 2013
  • Since 2000, a large number of molecular studies have been conducted in Hexapoda with generating large amount of mitochondrial sequences. In this study, to review mitochondrial COI sequences and their molecular studies reported in Hexapoda from 2000 to 2009, 488 molecular studies conducted based on 58,323 COI sequences were categorized according to 26 orders and the positions of COI sequences (5', 3', and entire regions). The numbers of molecular studies in which the three regions utilized varied largely among the 26 orders; however, seven orders showed preferred positions of COI sequences in the researches: Diptera and Orthoptera revealed the largest number of studies in the 5' region; while, Coleoptera, Phthiraptera, Odonata, Phasmatodea, and Psocoptera, showed the largest number of studies in the 3' region. From comparing 84 molecular studies published before 2000, we observed the possibilities that molecular studies in Coleoptera, Diptera, Phthiraptera, and Phasmatodea from 2000 to 2009 had been followed classical studies using the positions of COI sequences well-known until 1999. This study provides useful information to understand the overall trends in COI sequence usages as well as molecular studies conducted from 2000 to 2009 in Hexapoda.

The Correlation between the Precipitation considering Critical Infiltration and Groundwater Level in Ssangchun Watershed (한계침투링을 고려한 쌍천유역의 강수량과 지하수위의 상관관계)

  • Yang Jeong-Seok;Lim Chang-Hwa;Park Jae-Hyeon;Park Chang-Kun;Jeong Gyo-Cheol
    • The Journal of Engineering Geology
    • /
    • v.15 no.3
    • /
    • pp.303-307
    • /
    • 2005
  • Severe drawdown of Groundwater level(CWL) is observed from the analysis of the relationship between precipitation and CWL data during dry seasons in Ssangchun watershed. For Ssangchun watershed, the correlation was the strongest when we apply 70 day Moving Average(MA) for Groundwater dam Operation Index(COI) calculation. To determine the critical infiltration, which is the spatially averaged maximum daily infiltration, a certain value is fixed as the maximum infiltration and precipitation data is modified. COI is recalculated after the data modification and the correlation between COI and GWL is checked. The critical infiltration is determined when the best correlation is obtained after we repeat the above procedure with different fixed values. The critical infiltration is 40m for Ssangchun watershed. The correlation between CWL and COI is higher when we consider critical infiltration than we neglected it.

Geographic Genetic Contour of A Leaf Beetle, Chrysolina aurichalcea (Coleoptera: Chysomelidae), on the Basis of Mitochondrial COI Gene and Nuclear ITS2 Sequences

  • Park, Joong-Won;Park, Sun-Young;Wang, Ah-Rha;Kim, Min-Jee;Park, Hae-Chul;Kim, Ik-Soo
    • International Journal of Industrial Entomology
    • /
    • v.23 no.1
    • /
    • pp.155-166
    • /
    • 2011
  • The leaf beetle, $Chrysolina$ $aurichalcea$ (Coleoptera: Chysomelidae), is a pest damaging plants of Compositae. In order to understand the genetic diversity and geographic variation we sequenced a portion of mitochondrial COI gene (658 bp) and complete nuclear internal transcribed spacer 2 (ITS2) of the species collected from seven Korean localities. A total of 17 haplotypes (CACOI01~CACOI17), with the maximum sequence divergence of 3.04% (20 bp) were obtained from COI gene sequence, whereas 16 sequence types (ITS2CA01~ITS2CA16), with the maximum sequence divergence of 2.013% (9 bp) were obtained from ITS2, indicating substantially larger sequence divergence in COI gene sequence. Phylogenetically, the COI gene provided two haplotype groups with a high nodal support (${\geq}87%$), whereas ITS2 provided only one sequence type group with a high nodal support (${\geq}92%$). The result of COI gene sequence may suggest the presence of historical biogeographic barriers that bolstered genetic subdivision in the species. Different grouping pattern between COI gene and ITS2 sequences were interpreted in terms of recent dispersal, reflected in the ITS2 sequence. Finding of unique haplotypes and sequence types only from Beakryeng-Islet population was interpreted as an intact remnant of ancient polymorphism. As more samples are analyzed using further hyper-variable marker, further fruitful inference on the geographic contour of the species might be available.

Molecular identification and Phylogenetic relationship of the rook (Corvus frugilegus) population in Jeju-do Province, South Korea (제주도에 도래하는 떼까마귀 집단에 대한 분자 종 동정 및 계통 유연관계)

  • Han, Sang-Hyun;Kim, Tae-Wook;Kim, Yoo-Kyung;Park, Jun-Ho;Kim, Dong-Min;Adhikari, Preadeep;Park, Su-Gon;Park, Seon-Mi;Kim, Ga-Ram;Lee, Jun-Won;Oh, Hong-Shik
    • Korean Journal of Environment and Ecology
    • /
    • v.29 no.5
    • /
    • pp.693-702
    • /
    • 2015
  • In order to identify the species and to reveal the phylogenetic relationship of rook populations found in Jeju-do Province in winter seasons, we determined the sequences of mitochondrial cytochrome c oxidase I (COI) gene and analyzed the genetic structure of maternal lineages and phylogenetic relationship. The rook DNAs were isolated from the post-mortem specimens and plumages collected from agricultural farms in Jeju-do Province including U-do Island. The obtained COI sequences (n=41) showed over 97.0% identities with those previously reported from Corvus frugeligus. Three COI haplotypes (J01-J03) were detected from COI sequences of the rooks obtained in Jeju-do Province but those did not show the site-specific patterns, showing that they might be derived from a common maternal origin. Eight maternal haplotypes were detected from all COI sequences obtained. Among those three haplotypes contained the COI sequences from Northeast Asia including eastern Russia, Mongolia and South Korea. On the other hand, the other five haplotypes contained the COI sequences reported from Central Asia, Middle East, western Russia and European countries. The COI sequences from Jeju-do Province were located on three haplotypes (CF01-CF03) belonging to Northeast Asian rook lineages. The NJ tree showed the distinct branch patterns suggesting two different maternal lineages of C. frugilegus, which proposed as two parapatric subspecies, C. f. frugilegus (Western) and C. f. pastinator (Eastern). These findings using DNA barcoding approaches will be contributed to provide the information about avian fauna for understanding the genetic structure of maternal lineage, phylogenetic relationship and their molecular ecology.