• Journal of Species Research
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• 제2권1호
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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.

• Journal of Species Research
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• 제2권2호
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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).

• Animal Systematics, Evolution and Diversity
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• 제37권3호
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• pp.225-228
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• 2021

Eleven Gonioctena species have been recorded in the Korean Peninsula. Most species in the genus have very similar coloration and morphology. The male genitalia is generally used as the only reliable diagnostic character differentiating closely related species, but it is still difficult to identify females to species accurately. Here, we determined the COI barcodes of two Gonioctena species described from Korea and give morphological descriptions. The interspecific genetic divergence (Kimura 2-parameter) among the Gonioctena ranged from 0.073 to 0.138 and averaged 0.108. The pairwise genetic distance between the two Korean species(0.102) is similar to the average interspecific divergence. We predict that these analyses will help to resolve taxonomic issues and find cryptic species.

• 식물분류학회지
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• 제46권3호
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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.

• ALGAE
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• 제35권3호
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• pp.293-301
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• 2020

The applications of DNA barcoding have a wide range of uses, such as in taxonomic studies to help elucidate cryptic species and phylogenetic relationships and analyzing environmental samples for biodiversity monitoring and conservation assessments of species. After obtaining the DNA barcode sequences, sequence similarity-based homology analysis is commonly used. This means that the obtained barcode sequences are compared to the DNA barcode reference databases. This bioinformatic analysis necessarily implies that the overall quantity and quality of the reference databases must be stringently monitored to not have an adverse impact on the accuracy of species identification. With the development of next-generation sequencing techniques, a noticeably large number of DNA barcode sequences have been produced and are stored in online databases, but their degree of validity, accuracy, and reliability have not been extensively investigated. In this study, we investigated the extent to which the amount and types of erroneous barcode sequences were deposited in publicly accessible databases. Over 4.1 million sequences were investigated in three largescale DNA barcode databases (NCBI GenBank, Barcode of Life Data System [BOLD], and Protist Ribosomal Reference database [PR2]) for four major DNA barcodes (cytochrome c oxidase subunit 1 [COI], internal transcribed spacer [ITS], ribulose bisphosphate carboxylase large chain [rbcL], and 18S ribosomal RNA [18S rRNA]); approximately 2% of erroneous barcode sequences were found and their taxonomic distributions were uneven. Consequently, our present findings provide compelling evidence of data quality problems along with insufficient and unreliable annotation of taxonomic data in DNA barcode databases. Therefore, we suggest that if ambiguous taxa are presented during barcoding analysis, further validation with other DNA barcode loci or morphological characters should be mandated.

• Genomics & Informatics
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• 제10권3호
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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.

• 대한본초학회지
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• 제29권6호
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• pp.35-43
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• 2014

Objectives : Official Arisaematis Rhizoma is described only three species, Arisaema amurnse, Arisaema erubescens, and Arisaema heterophyllum, in national Pharmacopoeia. However, other Arisaema species, Arisaema ringens, Arisaema takesimense and Arisaema serratum, also have been distributed as an inauthentic Arisaematis Rhizoma in the herbal market. To develop a reliable molecular authentication method for Arisaematis Rhizoma in species level, we analyzed DNA barcode regions using six Arisaema species. Methods : Thirty-eight samples of six Arisaema plants species (A. amurense, A. amurense f. serratum, A. heterophyllum, A. takesimense, and A. serratum) were collected from different habitate and nucleotide sequences of DNA barcode regions (rDNA-ITS, matK, and rbcL gene) were analyzed after PCR amplification. The species-specific sequences and phylogenetic relations were estimated using entire sequences of three DNA barcodes based on the analysis of ClastalW and UPGMA, respectively. Results : The comparative analysis of DNA barcode sequences were revealed inter-species specific nucleotides to distinguish the medicinal plant of Arisaema Rhizoma in species levels excluding between A. amurense and its subspecies (A. amurense f. serratum) and A. takesimense and A. serratum, respectively. However, we obtained sequence differences enough to discriminate authentic and inauthentic Arisaematis Rhizoma. Therefore, we suggest that these SNP type molecular genetic markers were an reliable method avaliable to identify official herbal medicines. Conclusions : These marker nucleotides could be useful to identify the official herbal medicines by providing definitive information that can identify original medicinal plant and distinguish from inauthentic adulterants and substitutes.

• Animal Systematics, Evolution and Diversity
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• 제36권2호
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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.

• Animal Systematics, Evolution and Diversity
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• 제28권4호
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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.

• 대한본초학회지
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• 제28권6호
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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.