• Title, Summary, Keyword: DNA barcodes

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DNA Barcoding of the Marine Protected Species Parasesarma bidens (Decapoda: Sesarmidea) from the Korean Waters

  • Kim, So Yeon;Yi, Chang Ho;Kim, Ji Min;Choi, Woo Yong;Kim, Hyoung Seop;Kim, Min-Seop
    • Animal Systematics, Evolution and Diversity
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    • v.36 no.2
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    • pp.159-163
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    • 2020
  • Parasesarma bidens(De Haan, 1835) has been designated as a marine protected species by the Act on conservation and management of marine ecosystems. This crab has been recorded only from Jeju-do and Geomun-do, Republic of Korea. In this study, we describe for the first time the mitochondrial cytochrome c oxidase subunit I(COI) sequences of P. bidens. The intra-specific genetic distance among the Korean populations and between the Korean and Chinese populations ranged from 0% to 0.9% and 1.9% to 2.7%, respectively. The inter-specific genetic distances among the four Parasesarma species ranged from 10.9% to 12.8%. The finding of this study will be helpful to better describe P. bidens using COI DNA barcodes and can be used as basic data for their restoration and conservation research.

New record of two feather mites(Acari: Sarcoptiformes: Astigmata) isolated from Actitis hypoleucos in South Korea

  • Han, Yeong-Deok;Min, Gi-Sik
    • Journal of Species Research
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    • v.8 no.2
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    • pp.225-232
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    • 2019
  • Two feather mites, Bychovskiata hypoleuci Mironov and Ddabert, 1997 and Phyllochaeta interifolia (Mégnin and Trouessart, 1884) are reported for the first time in South Korea. Specimens of these two species were collected from the common sandpiper Actitis hypoleucos. The genera Bychovskiata Dubinin, 1951 and Phyllochaeta Dubinin, 1951 are also new reports for South Korea. Here, we provide morphological descriptions and illustrations of these two species. Additionally, we provide partial sequences of the mitochondrial cytochrome c oxidase subunit I(COI) as DNA barcodes.

Two New Eisenia Species from South Korea Similar to E. koreana and Comparable to Eisenoides from USA (Oligochaeta: Lumbricidae)

  • Blakemore, Robert J.;Park, Tae Seo
    • Animal Systematics, Evolution and Diversity
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    • v.28 no.4
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    • pp.297-303
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    • 2012
  • New Korean lumbricids are described: Eisenia gaga Blakemore sp. nov. from remote Gageodo Island and E. sindo Blakemore, sp. nov. from an island at Incheon. Both are comparable to Eisenia koreana (Zicsi, 1972) from near Pyongyang, North Korea. A remarkable yet previously unrecognized similarity to American earthworm Eisenoides carolinensis (Michaelsen, 1910) is discussed, but synonymy is rejected on tenuous morphological grounds (form of nephridial vesicle bladders) with taxonomy supported by objective molecular data (mtDNA cytochrome c oxidase subunit 1 barcodes).

Jeju-do earthworms (Oligochaeta: Megadrilacea)-Quelpart Island revisited

  • Blakemore, Robert J.
    • Journal of Species Research
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    • v.2 no.1
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    • pp.15-54
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    • 2013
  • Surveys on Jeju-do (Quelpart Isl.) unearthed about 40 earthworm species or sub-species. Several considered new to science are described. Only a dozen were previously known and these are taxonomically reviewed. The two most commonly recorded in surveys by S. Kobayashi in the 1930s were Drawida anchingiana Chen, 1933 and Metaphire quelparta (Kobayashi, 1937), neither recently relocated. Morphologically similar taxa, supported with DNA barcodes, for Moniligastridae, are Drawida anchingiana seogwipo, D. anchingiana halla and D. iucn spp. or sub-spp. nov. For Megascolecidae, new taxa and synonyms are: Amynthas arx and A. aucklandis spp. nov. that have seminal grooves rather than the eversible male pores of Metaphire plus Amynthas simplex is another new species. Amynthas sangumburi Hong & Kim, 2002 is recognized as a probable new synonym within the A. corticis (Kinberg, 1867) species-group while Amynthas corticis saeseum sub-sp nov. is described. Amynthas gracilis (Kinberg, 1867) is a new record from Jeju and Korea (with A. bouchei, A. omodeoi and A. edwardsi all by Zhao & Qiu, 2009 possible synonyms of this species group from China) with a Jejuan sub-species, A. gracilis insularum, sub-sp. nov. Presence on Jeju of Amynthas carnosus (Goto & Hatai, 1899) is confirmed (its further new synonyms are Chinese A. fuscus Qiu & Sun, 2012 and A. taiwumontis Shen et al., 2013), as is A. micronarius (Goto & Hatai, 1898) (with new synonym A. montanus Qiu & Sun, 2012 also an invalid secondary homonym). Amynthas phaselus maculosus (Hatai, 1930) is in new combination with A. kamitai (Kobayashi, 1934) and A. minjae Hong, 2001 syns. nov. Two newly described Metaphire quelparta sub-spp are M. q. seogwipo and M. q. valhalla these being supported with DNA barcodes despite the nominal taxon not yet being confirmed.

Survey of Busan Oligochaeta earthworms supported by DNA barcodes

  • Blakemore, Robert J.;Lee, Seunghan
    • Journal of Species Research
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    • v.2 no.2
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    • pp.127-144
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    • 2013
  • An earthworm survey of Busan metropolitan area unearthed a dozen taxa in four families (including Enchytraeidae). Members of mostly common, cosmopolitan earthworm species-complexes were: Drawida cf. koreana Kobayashi, 1938, Amynthas cf. corticis (Kinberg, 1867), Aporrectodea trapezoides (Dug$\grave{e}$s, 1828) and Eisenia fetida (Savigny, 1826). Also found were Amynthas hupeiensis (Michaelsen, 1895), A. masatakae (Beddard, 1892) and Metaphire ryunome Blakemore, 2012 - the latter a new Korean record. New taxa are: moniligastrid Drawida songae yeongdo subsp. n.; megascolecid Amynthas carnosus roki subsp. n. which is compared to nominal taxon A. carnosus (Goto and Hatai, 1899) from Japan, to A. carnosus monstriferus (Kobayashi, 1936) stat. n. from Korea and to A. lichuanensis Wang and Qiu, 2005 stat. n. from China; plus lumbricid Eisenia japonica vaga subsp. n. deemed an objectively-based molecular taxon on its unique DNA COI gene barcode. Restoration of Eisenia xanthurus (Templeton, 1836) for E. andrei is mooted (in Appendix).

DNA barcoding of Schisandraceae in Korea (한국산 오미자과의 DNA 바코드)

  • Youm, Jung Won;Han, Sang-Wook;Seo, Seon Won;Lim, Chae Un;Oh, Sang-Hun
    • Korean Journal of Plant Taxonomy
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    • v.46 no.3
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    • pp.273-282
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    • 2016
  • The establishment of a DNA barcode database at the regional scale and assessments of the utility of DNA barcodes are crucial for conservation biology and for the sustainable utilization of biological resources. Schisandraceae is a small family consisting of ca. 45 species. It contains many economically important species, such as Schisandra chinensis, which is widely used as a source in tonic beverages and in oriental medicine. In Korea, three species, S. chinensis, S. repanda, and Kadsura japonica, are distributed. We evaluated the level of variation of the DNA sequences of rbcL, matK, and the ITS regions from 13 accessions representing the distributional range of the three species. The three DNA barcode regions were easily amplified and sequenced. The minimum values of the interspecific genetic distances among S. chinensis, S. repanda, and K. japonica either separately or in combination are 4- to 23-fold higher than the maximum value of the intraspecific distance, showing that there is a clear DNA barcoding gap in the regions for Korean Schisandraceae. Phylogenetic analyses of the three DNA barcode regions, separately and simultaneously, indicate that all of the DNA barcode regions are useful for identifying a species of Schisandraceae in Korea. The distinctiveness of the three species of Schisandraceae was also supported at the species level when Chinese and Japanese populations were added. The results of this study indicate that three concatenated regions constitute the best option for DNA barcoding in Schisandraceae in Korea.

DNA Barcoding of Fish, Insects, and Shellfish in Korea

  • Kim, Dae-Won;Yoo, Won-Gi;Park, Hyun-Chul;Yoo, Hye-Sook;Kang, Dong-Won;Jin, Seon-Deok;Min, Hong-Ki;Paek, Woon-Kee;Lim, Jeong-Heui
    • Genomics & Informatics
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    • v.10 no.3
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    • pp.206-211
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    • 2012
  • DNA barcoding has been widely used in species identification and biodiversity research. A short fragment of the mitochondrial cytochrome c oxidase subunit I (COI) sequence serves as a DNA bio-barcode. We collected DNA barcodes, based on COI sequences from 156 species (529 sequences) of fish, insects, and shellfish. We present results on phylogenetic relationships to assess biodiversity the in the Korean peninsula. Average GC% contents of the 68 fish species (46.9%), the 59 shellfish species (38.0%), and the 29 insect species (33.2%) are reported. Using the Kimura 2 parameter in all possible pairwise comparisons, the average interspecific distances were compared with the average intraspecific distances in fish (3.22 vs. 0.41), insects (2.06 vs. 0.25), and shellfish (3.58 vs. 0.14). Our results confirm that distance-based DNA barcoding provides sufficient information to identify and delineate fish, insect, and shellfish species by means of all possible pairwise comparisons. These results also confirm that the development of an effective molecular barcode identification system is possible. All DNA barcode sequences collected from our study will be useful for the interpretation of species-level identification and community-level patterns in fish, insects, and shellfish in Korea, although at the species level, the rate of correct identification in a diversified environment might be low.

Exploring the Utility of Partial Cytochrome c Oxidase Subunit 1 for DNA Barcoding of Gobies

  • Jeon, Hyung-Bae;Choi, Seung-Ho;Suk, Ho Young
    • Animal Systematics, Evolution and Diversity
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    • v.28 no.4
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    • pp.269-278
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    • 2012
  • Gobiids are hyperdiverse compared with other teleost groups, with about 2,000 species occurring in marine, freshwater, and blackish habitats, and they show a remarkable variety of morphologies and ecology. Testing the effectiveness of DNA barcodes on species that have emerged as a result of radiation remains a major challenge in evolutionary biology. Here, we used the cytochrome c oxidase subunit 1 (COI) sequences from 144 species of gobies and related species to evaluate the performance of distance-based DNA barcoding and to conduct a phylogenetic analysis. The average intra-genus genetic distance was considerably higher than that obtained in previous studies. Additionally, the interspecific divergence at higher taxonomic levels was not significantly different from that at the intragenus level, suggesting that congeneric gobies possess substantial interspecific sequence divergence in their COI gene. However, levels of intragenus divergence varied greatly among genera, and we do not provide sufficient evidence for using COI for cryptic species delimitation. Significantly more nucleotide changes were observed at the third codon position than that at the first and the second codons, revealing that extensive variation in COI reflects synonymous changes and little protein level variation. Despite clear signatures in several genera, the COI sequences did resolve genealogical relationships in the phylogenetic analysis well. Our results support the validity of COI barcoding for gobiid species identification, but the utilization of more gene regions will assist to offer a more robust gobiid species phylogeny.

Molecular Authentication of Pinelliae Tuber from its adulterants by the analysis of DNA barcodes, matK and rbcL genes (matK와 rbcL DNA 바코드 분석을 통한 반하(半夏) 및 반하(半夏) 유사 한약재 유전자 감별)

  • Lee, Young Mi;Moon, Byeong Cheol;Ji, Yunui;Kim, Wook Jin;Kim, Ho Kyoung
    • The Korea Journal of Herbology
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    • v.28 no.6
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    • pp.53-58
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    • 2013
  • Objectives : Pinelliae Tuber has been used as a typical unauthentic herbal medicines. Due to the morphological similarity between Pinelliae Tuber and adulterants, the correct authentication is very difficult. Therefore, we introduced DNA barcode to establish a powerful tool for the authentication of Pinelliae Tuner from adulterants. Methods : To obtain DNA barcode regions, genomic DNA was extracted from nineteen specimens of Pinellia ternata, Pinellia pedatisecta, Pinellia tripartita, and Typhonium flagelliforme, and matK and rbcL genes were amplified. For identification of species specific sequences and analysis phylogenetic relationship, a comparative analysis were performed by the ClastalW and UPGMA based on entire sequences of matK and rbcL genes, respectively. Results : In comparison of two DNA barcode sequences, we elucidated the phylogenetic relationship showing distinct four groups depending on species and identified 40 and 20 species specific nucleotides enough to distinguish each species from matK and rbcL gene, respectively. The sequence differences at the corresponding positions were avaliable genetic marker nulceotides to discriminate the correct species among analyzed four species. These results indicated that phylogentic and comparative analysis of matK and rbcL genes are useful genetic markers to authenticate Pinelliae Tubers. Conclusions : The marker nucleotides enough to distinguish P. ternata, P. tripatrita, P. peditisecta, and T. flagelliform, were observed at 40 positions in matK gene and 20 positions in rbcL gene sequence, respectively. These differences can be used to authenticate Pinelliae Tuber from adulterants as well as discriminate each four species.

Study on Molecular Phylogenetics of Korean Arisaema Species Based on Universal DNA Barcodes (범용성 DNA 바코드 분석 기반 한국산 천남성속(Arisaema) 식물의 분자계통학적 연구)

  • Noh, Pureum;Han, Kyeongsuk;Kim, Wook Jin;Yang, Sungyu;Choi, Goya;Ko, Sung Chul;Moon, Byeong Cheol
    • Korean Journal of Plant Resources
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    • v.31 no.1
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    • pp.37-51
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    • 2018
  • Molecular phylogenetic analysis was conducted to evaluate the taxonomic relationships of genus Arisaema L. distributed in Korea and the molecular phylogenetic characteristics of three authentic Arisaema species for the herbal medicine Arisaematis Rhizoma (the rhizomes of A. amurense, A. heterophyllum, and A. erubescens). The sequences of three DNA barcodes (rDNA-ITS, matK, and rbcL) were analyzed using 50 samples of nine taxa consisted of eight Korean and one Chinese Arisaema with one outgroup (Dracunculus vulgaris). Both individual and combined phylogenetic analyses of three DNA barcode sequences revealed that the treated nine taxa are independently classified into six distinct clades (Clade I, A. amurense f. amurense and A. amurense f. serratum; Clade II, A. serratum and A. takesimense; Clade III, A. ringens; Clade IV, A. erubescens; Clade V, A. heterophyllum; Clade VI, A. thunbergii subsp. thunbergii and A. thunbergii subsp. geomundoense). These six clades were reasonably divided into three individual sections, Pedatisecta, Sinarisaema, and Tortuosa. Futhermore, the results of comparative DNA barcode sequences analyses provided a significant information for the taxonomic reconsideration of Arisaema L. at the specific and intraspecific level. However, we could not confirm the taxonomic characteristics or identity among the three authentic medicinal species through the molecular phylogenetic analyses of genus Arisaema L. for Arisaematis Rhizoma.