• Mycobiology
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• v.48 no.5
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• pp.331-340
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• 2020

The family Peronosporaceae, an obligate biotrophic group of Oomycota, causes downy mildew disease on many cultivated and ornamental plants such as beet, cucumber, grape, onion, rose, spinach, and sunflower. To investigate the diversity of Peronosporaceae species in Korea, we performed morphological analysis for dried plant herbariums with downy mildew infections by two largest genera, Peronospora and Plasmopara. As a result, it was confirmed that there are five species of Peronospora and two species of Plasmopara, which have been so far unrecorded in Korea, as well as rarely known in the world; Pl. angustiterminalis (ex Xanthium strumarium), Pl. siegesbeckiae (ex Siegesbeckia glabrescens), P. chenopodii-ambrosioidis (ex Chenopodium ambrosioides), P. chenopodii-ficifolii (ex Chenopodium ficifolium), P. clinopodii (ex Clinopodium cf. vulgare), P. elsholtziae (ex Elsholtzia ciliata), and P. lathyrina (ex Lathyrus japonicus). In addition, their phylogenetic relationship was inferred by molecular sequence analysis of ITS, LSU rDNA, and cox2 mtDNA. By rediscovering the seven missing species and barcoding their DNA sequences, this study provides valuable insights into the diversity and evolutionary studies of downy mildew pathogens.

• Mycobiology
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• v.41 no.4
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• pp.191-201
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• 2013

Distinguishing individual Russula species has been difficult due to extensive phenotypic plasticity and obscure morphological and anatomical discontinuities. Due to highly similar macroscopic features, such as the presence of a red-cap, species identification within the Russula subgenus Amoenula is particularly difficult. Three species of the subgenus Amoneula have been reported in Korea. We used a combination of morphology and three molecular markers, the internal transcribed spacer (ITS), 28S nuclear ribosomal large subunit (LSU), and RNA polymerase II gene (RPB2), for identification and study of the genetic diversity of Russula subgenus Amoenula in Korea. We identified only two species in Korea (R. mariae and R. violeipes); these two species were indistinguishable according to morphology and LSU, but were found to be reciprocally monophyletic species using ITS and RPB2. The markers, ITS, LSU, and RPB2, have been tested in the past for use as DNA barcoding markers, and findings of our study suggest that ITS and RPB2 had the best performance for the Russula subgenus Amoneula.

• Fisheries and Aquatic Sciences
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• v.21 no.3
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• pp.8.1-8.6
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• 2018

Desmarestia japonica (Phaeophyceae, Desmarestiales) was recently established from the Japanese ligulate Desmarestia and is morphologically similar to D. ligulata. This species has been reported only from Japan. However, the taxonomic reports based on additional regional distributions are needed to clarify this taxonomic entity and its species boundaries. Because Desmarestia species have restricted distributions in Korea, we reexamined herbarium specimens of D. ligulata deposited at the National Institute of Biological Resources (South Korea). To improve the amplification efficiency of the polymerase chain reaction and avoid contamination by the DNA of other organisms, we developed taxon-specific molecular markers suitable for DNA barcoding of Desmarestia species. Nuclear ribosomal small subunit RNA (18S rDNA) and mitochondrial cytochrome c oxidase 1 (cox1) regions were selected as target DNA. As a result, both were successfully isolated from herbarium specimens of D. japonica acquired over 10 years. These molecular markers provide useful genetic information for herbarium specimens for which conventional molecular analysis is challenging.

• Korean Journal of Plant Taxonomy
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• v.41 no.3
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• pp.209-214
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• 2011

The taxonomy of the umbelliferous species Angelica amurensis and its allies was reviewed on the basis of molecular phylogenies derived from sequences of nuclear ribosomal DNA internal transcribed spacer (ITS) regions. Strict consensus of six minimal length 119-step trees derived from equally weighted maximum parsimony analysis of combined nuclear rDNA ITS1 and ITS2 sequences from 29 accessions of Angelica and outgroups indicated that Angelica purpuraefolia, known to be endemic to Korea, is the same species as A. amurensis. Comparisons of sequence pairs across both spacer regions revealed identity or 1-2 bp differences between A. purpuraefolia and A. amurensis. These results indicated that the two taxa are not distinguished taxonomically. Also, nuclear rDNA ITS regions are discussed as potential barcoding loci for identifying Korean Angelica.

• Journal of the Korean Society of Fisheries and Ocean Technology
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• v.56 no.4
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• pp.316-321
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• 2020

A single juvenile malacanthid specimen (Hoplolatilus chlupatyi) was collected from the South Sea of Korea and identified by DNA barcoding. This species is readily distinguished from other malacanthid species in having well developed rostral spine and elongated spines in the posttemporal and preopercle. A molecular analysis based on mitochondrial DNA COI sequences showed that this species is matched to adult H. chlupatyi (genetic distance = 0.005). Therefore, this is the first record of H. chlupatyi in Korea. We propose new Korean names, "Mu-ji-gae-og-dom-sog" for the genus Hoplolatilus and "Mu-ji-gae-og-dom" for the species H. chlupatyi.

• Animal Systematics, Evolution and Diversity
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• v.35 no.4
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• pp.186-190
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• 2019

DNA barcoding of two marine tintinnids, Eutintinnus rectus and Schmidingerella arcuata, was performed using four samples collected from different sites in the north-eastern coast of South Korea. The loricae morphology was observed by light and scanning electron microscopy. Molecular data were analyzed using five nuclear ribosomal DNA markers(18S, ITS1, 5.8S, ITS2, and 28S genes) and one mitochondrial marker (CO1 gene). The intraspecific pairwise differences of E. rectus and S. arcuata in the CO1 gene were 0.0-0.2% and 0.0-0.6%, respectively, while there were no differences in the 18S rDNA sequences.

• Animal Systematics, Evolution and Diversity
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• v.38 no.3
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• pp.144-147
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• 2022

The polychaete Scolelepis (Scolelepis) sagittaria was originally described from Japanese waters and subsequently reported from Korean waters. In this study, we determined for the first time the mitochondrial cytochrome c oxidase subunit I (COI), 16S ribosomal DNA (16S rDNA), and nuclear 18S ribosomal DNA (18S rDNA) sequences of Korean specimens of S. (S.) sagittaria. We also assessed intraspecific variation in the shape of the prostomium of this species based on an examination of 247 individuals. All materials were collected from intertidal sandy beaches of the Korea Strait. The molecular data and morphological observations reported herein will contribute to gaining a better understanding of the taxonomic relationships among members of the genus Scolelepis.

• ALGAE
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• v.28 no.1
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• pp.31-43
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• 2013

This review provides a comprehensive summary of the PCR primers and profiles currently in use in our laboratory for red algal DNA barcoding and phylogenetic research. While work focuses on florideophyte taxa, many of the markers have been applied successfully to the Bangiales, as well as other lineages previously assigned to the Bangiophyceae sensu lato. All of the primers currently in use with their respective amplification profiles and strategies are provided, which can include full fragment, overlapping fragments and what might best be called "informed overlapping fragments", i.e., a fragment for a marker is amplified and sequenced for a taxon and those sequence data are then used to identify the best primers to amplify the remaining fragment(s) for that marker. We extend this strategy for the more variable markers with sequence from the external PCR primers used to "inform" the selection of internal sequencing primers. This summary will hopefully serve as a useful resource to systematists in the red algal community.

• Korean Journal of Environmental Biology
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• v.41 no.2
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• pp.145-166
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• 2023

Parrots have been threatened by global trade to meet their high demand as pets. Controlling parrot trade is essential because parrots play a vital role in the ecosystem. Accurate species identification is crucial for controlling parrot trade. Parrots have been traded as eggs due to their advantages of lower mortality rates and more accessible transport than live parrots. A molecular method is required to identify parrot eggs because it is difficult to perform identification using morphological features. In this study, DNAs were obtained from 43 unidentified parrot eggs using a non-destructive sampling method. Partial cytochrome b (CYTB) gene was then successfully amplified using polymerase chain reaction (PCR) and sequenced. Sequences newly obtained in the present study were compared to those available in the GenBank by database searching. In addition, phylogenetic analysis was conducted to identify species using available sequences in GenBank along with sequences reported in previous studies. Finally, the 43 parrot eggs were successfully identified as seven species belonging to two families and seven genera. This non-destructive sampling method for obtaining DNA and molecular identification might help control the trade of parrot eggs and prevent their illegal trade.

• 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.