• Animal Systematics, Evolution and Diversity
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• v.36 no.3
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• pp.258-263
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• 2020

The aim of this study is to report monotypic species, Nonparahalosydna pleiolepis(Marenzeller, 1879) for the first time from Korean waters with its DNA barcoding data. We collected individuals of the species from the subtidal zone of southern coast of Korea through scuba diving. To estimate DNA barcoding gap, the pairwise genetic distances were calculated between N. pleiolepis and its congeners (Halosydna brevisetosa Kinberg, 1856 and Lepidonotus squamatus (Linnaeus, 1758)) based on the cytochrome c oxidase subunit I gene (COI). Inter-specific genetic distances ranged from 18.7% to 24.6%, while intra-specific genetic distance within N. pleiolepis ranged from 0.3% to 0.5%. The maximum intra-specific genetic distance among the three species was 1.4%. The morphological diagnosis of N. pleiolepis with a taxonomic note on the species were also provided.

• Korean Journal of Plant Taxonomy
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• v.46 no.2
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• pp.163-174
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• 2016

Gnetum (Gnetaceae, Gnetales) is a gymnosperm genus with ca. 35 species distributed in tropical forests around the world. Due to its dioecious habit and lack of diagnostic characters from vegetative tissue, the identification of Gnetum species is not easy without seeds or reproductive structures. To identify and verify their phylogenetic positions, we applied DNA barcoding to Cambodian Gnetum collections gathered between 2010 and 2015, with previously designed cp matK gene primers. We newly sequenced partial matK sequences from 72 Gnetum collections, 43 out of 72 from Cambodia, and analyzed 115 Gnetum accessions using the neighbor-joining method. The resulting neighbor-joining tree categorized Cambodian Gnetum samples into three clades of species: G. macrostachyum, G. montanum, and G. aff. gracilipes. The recognition of G. aff. gracilipes in Cambodia is reported here for the first time. Taxonomic information for the three recognized Cambodian Gnetum species is provided and the benefits of the taxonomic reevaluation assisted by DNA barcoding are emphasized in this work.

• Journal of Species Research
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• v.9 no.4
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• pp.413-426
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• 2020

The Euphorbiaceae family features some of the most economically important plants that are sources of foods, oils, waxes, and medicines. The accurate identification of Euphorbiaceae species is critical in sustainable utilization of plant resources. We examined 234 sequences of nrDNA ITS, cpDNA rbcL and matK loci from 20 species in Euphorbiaceae in Korea and three outgroup taxa to develop efficient DNA barcodes. The three barcode loci were successfully amplified and sequenced for all Euphorbiaceae species. nrDNA ITS locus showed the highest mean interspecific K2P distance (0.3034), followed by cpDNA matK (0.0830), and rbcL (0.0352) locus. The degree of species resolution for individual barcode loci ranged from 75% (rbcL and matK) to 80% (ITS). The degree of species resolution was not enhanced with the different combinations of three barcode loci. The combined data set of the three loci(ITS+rbcL+matK) provided 80% of species resolution. These results confirm that ITS locus, as a single barcode, is the best option for barcoding of the Euphorbiaceae in Korea.

• Korean Journal of Medicinal Crop Science
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• v.23 no.6
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• pp.439-445
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• 2015

Background : Correct identification of Panax species is important to ensure food quality, safety, authenticity and health for consumers. This paper describes a high resolution melting (HRM) analysis based method using internal transcribed spacer (ITS) and 5.8S ribosomal DNA barcoding regions as target (Bar-HRM) to obtain barcoding information for the major Panax species and to identify the origin of ginseng plant. Methods and Results : A PCR-based approach, Bar-HRM was developed to discriminate among Panax species. In this study, the ITS1, ITS2, and 5.8S rDNA genes were targeted for testing, since these have been identified as suitable genes for use in the identification of Panax species. The HRM analysis generated cluster patterns that were specific and sensitive enough to detect small sequence differences among the tested Panax species. Conclusion : The results of this study show that the HRM curve analysis of the ITS regions and 5.8S rDNA sequences is a simple, quick, and reproducible method. It can simultaneously identify three Panax species and screen for variants. Thus, ITS1HRM and 5.8SHRM primer sets can be used to distinguish among Panax species.

• Fisheries and Aquatic Sciences
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• v.16 no.1
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• pp.45-48
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• 2013

A juvenile of the slender fangjaw, Sigmops gracilis G$\ddot{u}$nther, 1878 (Stomiiformes: Gonostomatidae) was collected from Jeju Island, Korea, and identified by DNA barcoding. This species is characterized by its large curved mouth and the presence of 11 dorsal fin rays and 28 anal fin rays. During the juvenile stage, the species is distinguished from other gonostomatid species by the position of the origin of the dorsal fin, which is located at the 7th-8th ray of the anal fin. The Korean name "Sol-ni-ael-tung-i" is proposed for this species.

• 한국균학회소식:학술대회논문집
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• 2014.05a
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• pp.17-17
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• 2014

Over five thousand higher fungal specimens were collected from 32 forest areas of Chungcheong and Gyeongsang province from 2012 to 2013. We obtained 513 strains and 3,120 ITS sequences. Mushrooms were first identified with macro- and micro-scopic characters, and their identification was confirmed on the basis of ITS sequences. Voucher specimens were designated for each species found in Korea. Construction of DNA barcoding Database is currently underway with sequences of 409 species. During the development of the database, some new species were recognized, along with several Korean new records. When the system has been completed, it will provide essential molecular information for metagenomic and phylogenetic researches for higher fungi.

• Korean Journal of Plant Taxonomy
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• v.43 no.4
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• pp.252-262
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• 2013

During the floristic survey on Phnom Bokor National Park, Kampot, Cambodia, we encountered Balanophora fungosa var. indica, which is a tropical holoparasitic plant. To identify its host species, we collected host roots and trees nearby and tried to identify them using DNA barcoding approach. We applied plastid rbcL and matK gene regions as DNA barcode markers, and successfully amplified and sequenced the markers from 15 host roots and seven tree samples. Obtained host root sequences were identified as Primulaceae, Celastraceae, Myrtaceae, and Oleaceae, while trees nearby are Oleaceae, Myrtaceae, Sapindaceae, Rosaceae, Clusiaceae, Ericaceae, and Lauraceae. At genus level, host species are identified as Myrsine, Euonymus, Syzygium, and Olea, but failed in species discrimination. Myrsine (Primulaceae) and Olea (Oleaceae) are reported here as host species of B. fungosa var. indica for the first time. Further sampling and comparative work, and DNA barcoding will help recognize the biodiversity of the area and host species of Balanophora, together with their evolution.

• The Korea Journal of Herbology
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• v.34 no.4
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• pp.1-8
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• 2019

Objectives : Rosae Multiflorae Fructus is a traditional medicine derived from the fruit of Rosa multiflora Thunb. a member of the Rosaceae family. Even though it has a single origin, the possibility of adulterants has always existed. In fact, we had discovered suspicious commercial samples of Rosae Multiflorae Fructus, imported from China. Methods : To define the taxonomic origin of Rosae Multiflorae Fructus and its adulterants, DNA barcode analysis of the internal transcribed spacer, trnL-F intergenic spacer, and psbA-trnH sequences was carried out. These DNA barcode sequences from the correct origin of Rosae Multiflorae Fructus were analyzed and compared with those of other samples from genus Rosa used as medicinal herbs. Results : The analyses of the three DNA barcode sequences efficiently distinguished Rosae Multiflorae Fructus from six other species in genus Rosa and also separated each species used in this study. According to the DNA barcoding results, none of the suspicious commercial samples were Rosae Multiflorae Fructus. RMF09 was identified as Rosa acicularis, whereas RMF10 and RMF11 were identified as Rosa davurica and Rosa rugosa, respectively. These results corroborated the existence of adulterants of Rosae Multiflorae Fructus. Conclusions : Our research provides useful information that could be used as a criterion for distinguishing between Rosae Multiflorae Fructus and its adulterants. These results will help in the prevention of adulteration and also suggest effective methods for verifying the origin of commercial herbal medicines derived from genus Rosa.

• Genomics & Informatics
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• v.21 no.3
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• pp.39.1-39.15
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• 2023

DNA barcoding without assessing reliability and validity causes taxonomic errors of species identification, which is responsible for disruptions of their conservation and aquaculture industry. Although DNA barcoding facilitates molecular identification and phylogenetic analysis of species, its availability in clariid catfish lineage remains uncertain. In this study, DNA barcoding was developed and validated for clariid catfish. 2,970 barcode sequences from mitochondrial cytochrome c oxidase I (COI) and cytochrome b (Cytb) genes and D-loop sequences were analyzed for 37 clariid catfish species. The highest intraspecific nearest neighbor distances were 85.47%, 98.03%, and 89.10% for COI, Cytb, and D-loop sequences, respectively. This suggests that the Cytb gene is the most appropriate for identifying clariid catfish and can serve as a standard region for DNA barcoding. A positive barcoding gap between interspecific and intraspecific sequence divergence was observed in the Cytb dataset but not in the COI and D-loop datasets. Intraspecific variation was typically less than 4.4%, whereas interspecific variation was generally more than 66.9%. However, a species complex was detected in walking catfish and significant intraspecific sequence divergence was observed in North African catfish. These findings suggest the need to focus on developing a DNA barcoding system for classifying clariid catfish properly and to validate its efficacy for a wider range of clariid catfish. With an enriched database of multiple sequences from a target species and its genus, species identification can be more accurate and biodiversity assessment of the species can be facilitated.

• 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.