• 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.

• The Korea Journal of Herbology
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• v.30 no.3
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• pp.41-47
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• 2015

Objectives : Due to the morphological similarity of the pericarp and description of multi-species in National Pharmacopoeia of Korea and China, the Zanthoxylum Pericarpium is difficult to authenticate adulterant in species levels. Therefore, we introduced the sequence analysis of DNA barcode and identification of single nucleotide polymorphism(SNP) to establish a reliable tool for the distinction of Zanthoxylum Pericarpium from its adulterants. Methods : To analyze DNA barcode region, genomic DNA was extracted from twenty-four specimens of authentic Zanthoxylum species and inauthentic adulterant and the individual internal transcribed spacer regions (rDNA-ITS and ITS2) of nuclear ribosomal RNA gene were amplified using ITS1, ITS2-S2F, and ITS4 primer. For identification of species-specific sequences, a comparative analysis was performed using entire DNA barcode sequences. Results : In comparison of four Zanthoxylum ITS2 sequences, we identified 16, 4, 6, and 4 distinct species-specific nucleotides enough to distinguish Z. schinifolium, Z. bungeanum, Z. piperitum, and Z. simulans, respectively. The sequence differences were available genetic marker to discriminate four species. Futhermore, phylogenetic relationship revealed a clear classification between different Zanthoxylum species showing 4 different clusters. These results indicated that comparative analysis of ITS2 DNA barcode was an useful genetic marker to authenticate Zanthoxylum Pericarpium in species levels. Conclusions : The marker nucleotides, enough to distinguish Z. schinifolium, Z. piperitum, Z. bungeanum, and Z. simulans, were obtained at 30 SNP marker nucleotides from ITS2 sequences. These differences could be used to authenticate official Zanthoxylum Pericarpium from its adulterants as well as discriminating each four species.

• Animal Systematics, Evolution and Diversity
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• v.27 no.2
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• pp.159-163
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• 2011

DNA barcoding of Bryozoa or "moss animals" has hardly advanced and lacks reference sequences for correct species identification. To date only a small number of cytochrome c oxidase subunit I (COI) sequences from 82 bryozoan species have been deposited in the National Center for Biotechnology Information (NCBI) GenBank and Barcode of Life Data Systems (BOLD). We here report COI data from 53 individual samples of 29 bryozoan species collected from Korean seawater. To our knowledge this is the single largest gathering of COI barcode data of bryozoans to date. The average genetic divergence was estimated as 23.3% among species of the same genus, 25% among genera of the same family, and 1.7% at intraspecific level with a few rare exceptions having a large difference, indicating a possibility of presence of cryptic species. Our data show that COI is a very appropriate marker for species identification of bryozoans, but does not provide enough phylogenetic information at higher taxonomic ranks. Greater effort involving larger taxon sampling for the barcode analyses is needed for bryozoan taxonomy.

• Weed & Turfgrass Science
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• v.4 no.1
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• pp.18-25
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• 2015

A universal DNA barcoding for agricultural noxious weeds is a powerful technique for species identification without morphological knowledge, by using short sections of DNA from a specific region of the genome. Two standard barcode markers, chloroplast rbcL and matK, and a supplementary nuclear ribosomal Internal Transcribed Spacer (ITS) region were used to examine the effectiveness of the markers for Pooideae barcoding using 163 individuals of 29 taxa across 16 genera of Korean Pooideae. The rbcL and ITS revealed a good level of amplification and sequencing success while matK did not. Barcode gaps were 78.6% for rbcL, 96.2% for matK, and 91.7% for ITS, respectively. Resolving powers were 89.3% for rbcL, 92.3% for matK, and 79.1% for ITS. The matK obtained the best both barcode gap and resolving power. However, it should be considered not to employ matK for Pooideae barcode because of low rate of PCR amplification and sequencing success. As a single DNA marker, rbcL and ITS were reasonable for Pooideae barcode. Barcode gap and resolving power were increased when ITS was incorporated into the rbcL. The barcode sequences were deposited to the National Center for Biotechnology Information (NCBI) database for public use.

• Molecules and Cells
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• v.22 no.3
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• pp.323-327
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• 2006

DNA barcoding, an inventory of DNA sequences from a standardized genomic region, provides a bio-barcode for identifying and discovering species. Several recent studies suggest that the sequence diversity in a 648 bp region of the mitochondrial gene for cytochrome c oxidase I (COI) might serve as a DNA barcode for identifying animal species such as North American birds, insects and fishes. The present study tested the effectiveness of a COI barcode in discriminating Korean bird species. We determined the 5' terminus of the COI barcode for 92 species of Korean birds and found that species identification was unambiguous; the genetic differences between closely related species were, on average, 25 times higher than the differences within species. We identified only one misidentified species out of 239 specimens in a genetic resource bank, so confirming the accuracy of species identification in the banking system. We also identified two potential composite species, calling for further investigation using more samples. The finding of large COI sequence differences between species confirms the effectiveness of COI barcodes for identifying Korean bird species. To bring greater reliability to the identification of species, increased intra- and interspecies sampling, as well as supplementation of the mitochondrial barcodes with nuclear ones, is needed.

• The Korea Journal of Herbology
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• v.28 no.3
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• pp.75-84
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• 2013

Objectives : The origin of Breeae Herba (So-gye) and Cirsii Herba (Dae-gye) is differently prescribed in Korean and Chinese modern pharmacopoeia. Since the similar morphological characteristics and chaotic plant names, moreover, the aerial part of Carduus crispus have been used as the Cirsii Herba. To develop a reliable method for correct identification of these herbal medicines and to evaluate the genetic relationship of these closely related plant species, we analyzed sequences of DNA barcode regions. Methods : Thirty-one samples of 6 medicinal plants (B. segeta, B. setosa, C. japonicum var. maackii, C. setidens, C. chanroenicum, and C. crispus) were collected from different habitate and nucleotide sequences of DNA barcode regions (rDNA-ITS, matK, and rbcL) were analyzed after amplification using appropriate primers reported in previous studies. The nucleotides of species-specific authentic marker and phylogenetic relations were estimated based on the entire sequences of DNA barcodes by the analysis of ClastalW and UPGMA, respectively. Results : In comparative analysis of DNA barcode sequences, we obtained specific nucleotides to discriminate the medicinal plant of Breeae/Cirsii Herba in species level and evaluated the phylogenetic relationship of these species. Futhermore, we identified distinct marker nucleotides enough to authenticate respective species. These sequence differences at corresponding positions were avaliable genetic markers to determine the botanical origins of Breeae Herbal as well as Cirsii Herba. Conclusions : These marker nucleotides would be useful to identify the official herbal medicines by providing of definitive information that can identify each plant species and distinguish from unauthentic adulterants and substitutes.

• 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.

• Journal of Ecology and Environment
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• v.34 no.3
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• pp.323-331
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• 2011

Biodiversity and the community composition of micro-eukaryotic organisms were investigated in the Upo wetland in Korea using molecular analysis. Molecular identification was performed using cytochrome oxidase I (COI) and small subunit ribosomal DNA (SSU rDNA). The genomic DNA was isolated directly from soil samples. The COI and SSU rDNA regions were amplified using universal primers and then sequenced after cloning. In a similarity search of the obtained sequences with BLAST in the Genbank database, the closely related sequences from NCBI were used to identify the amplified sequences. A total of six eukaryotic groups (Annelida, Arthropoda, Rotifera, Chlorophyta, Bacillariophyta, and Stramenopiles) with COI and six groups (Annelida, Arthropoda, Rotifera, Alveolata, Fungi, and Apicomplexa) with SSU rDNA genes were determined in the Upo wetland. Among 38 taxa in 20 genera, which are closely related to the amplified sequences, 10 genera (50%) were newly reported in Korea and five genera (25%) were shown to be distributed in the Upo wetland. This approach is applicable to the development of an efficient method for monitoring biodiversity without traditional taxonomic processes and is expected to produce more accurate results in depositing molecular barcode data in the near future.

• Animal Systematics, Evolution and Diversity
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• v.35 no.1
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• pp.37-39
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• 2019

We determined the cytochrome c oxidase subunit 1 (CO1) sequences of Nebalia koreana Song, Moreira & Min, 2012 (Leptostraca) collected from five locations in South Korea, and this represents the first genetic data of this species. The maximum intra-species variation was 1.2% within Nebalia hessleri Martin, Vetter & Cash-Clark, 1996, while inter-species variation ranged from 9.0% (N. hessleri and Nebalia gerkenae Haney & Martin, 2000) to 34.8% (N. hessleri and Nebalia pseudotroncosoi Song, Moreira & Min, 2013). This result is well agreed with the interspecific relationships among Nebalia species based on morphological characteristics. In conclusion, this study showed the usefulness of CO1 sequences as a DNA barcode within the genus Nebalia Leach, 1814.

• Animal Systematics, Evolution and Diversity
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• v.37 no.1
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• pp.1-8
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• 2021

A eunicid polychaete, Marphysa victori Lavesque, Daffe, Bonifácio & Hutchings, 2017 is described for the first time from the intertidal zones of the Korean coasts. It is characterized by having three types of pectinate chaetae (INS, isodont-narrow-slender; AWS, anodont-wide-slender; and AWT, anodont-wide-thick), appearance of pectinate chaetae from chaetiger 2, the chaetae consisted of pectinate and compound spinigers, and pygidium with one pair of pygidial cirri. In genetic analysis based on cytochrome c oxidase subunit I (COI), intra-specific genetic distance between the specimens of M. victori from its type locality, France and Korea are in the range of 0.000-0.013. This paper includes the morphological description and photographs of M. victori new to Korean fauna, with partial sequences of the mitochondrial COI as DNA barcode data on this species.