• International Journal of Industrial Entomology and Biomaterials
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• v.16 no.2
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• pp.75-86
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• 2008

In order to understand geographic genetic variation and relationship among populations of the mason bee (Osmia cornifrons Radoszkowsky), which is used as pollinator for apple tree, we sequenced a portion of mitochondrial (mt) COI gene, which corresponds to "DNA Barcode" region (658 bp) from 81 O. cornifrons individuals collected over eight localities in Korea. The sequence data revealed overall moderate to low genetic diversity within species, with a maximum sequence divergence of 0.76%. Geographically, two haplotypes (BAROC01 and BAROC02) were widespread with a frequency of 82.7%, whereas several haplotypes were found in a locality as a single individual, suggesting that haplotype distribution can be summarized as coexistence of a few widespread haplotypes and several regionally restricted haplotypes. Overall, high rate of per generation female migration (Nm=$1.1{\sim}$infinite) and low level of geographic subdivision ($F_{ST}=0{\sim}0.315$) among localities were characteristic. Although two populations (p < 0.026) were genetically subdivided from the remaining localities, no clear polarity was observed. Taken together, the nature of genetic divergence of the mason bee populations is characterized as one that possessing moderate to low genetic diversity, high gene flow, and wide spread haplotypes with ahigh frequency, concordant with the capability of dispersal in connection with the lack of historical biogeographic barriers.

• International Journal of Industrial Entomology and Biomaterials
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• v.22 no.2
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• pp.65-74
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• 2011

The Scarites aterrimus (Coleoptera: Carabidae), is one of the carabid beetles dwelling exclusively on coastal sandy dunes. Habitat deterioration and equivalent activity have greatly concerned population declines in several species dwelling on the coastal sandy dunes. As a first step to establish long-term conservation strategy, we investigated the nation-wide magnitude and nature of genetic diversity of the species. As a first step, we sequenced a portion of mitochondrial COI gene, corresponding to "DNA Barcode" region (658 bp) from a total of 24 S. aterrimus individuals collected over nine sandy dunes belonging to four Korean provinces. The sequence analysis evidenced moderate to low magnitude of sequence diversity compared with other insect species distributed in Korean peninsula (0.152% to 0.912%). The presence of closely related haplotypes and relatively high gene flow estimate collectively suggest that there had been no historical barriers that bolster genetic subdivision. Population decline was postulated on the basis of several missing haplotypes that are well found in the species with a large population size. This interpretation is consistent with field observation of small population size in the coastal sandy dune habitats. The highest genetic diversity estimates were found in the coastal sand dune population of Seogwipo, Jeju Island, justifying a prior attention to the population, in order to sustain overall genetic diversity of the species. Further scrutinized study might be required for further robust conclusion.

• Korean Journal of Organic Agriculture
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• v.27 no.3
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• pp.353-363
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• 2019

To identify four cyst nematodes (Heterodera schachtii, H. trifolii, H. glycines, H. sojae) that are economically important plant-parasitic nematodes in Korea, restriction fragment length polymorphism (RFLP) by 8 endonucleases (PstI, VspI, AlwI, RsaI, MvaI, EcoRI, Eco72I, Hinf I) was performed based on sequence difference of mitochondrial DNA cytochrome c oxidase subunit I (COI) gene. As a result, species-specific DNA band patterns by RsaI endonuclease were observed in H. schachtii. The specific patterns was in H. trifolii by 3 endonucleases (VspI, AlwI, Hinf I), and was in H. glycines by Hinf I. While, H. sojae was not digested by 4 endonuclease (VspI, AlwI, RsaI, Hinf I). This study showed that four cyst nematodes could be distinguished using RFLP by 4 endonucleases (RsaI, VspI, AlwI, Hinf I) based on the sequence difference of COI gene.

• Fisheries and Aquatic Sciences
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• v.25 no.12
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• pp.637-647
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• 2022

A spotted scat, Scatophagus argus, has a high nutritional value and is among Asia's most widely consumed fish species. Thua Thien Hue's consumption market considers this species to be of high economic value and requires protection and conservation of the population. However, the studies on the identification and genetic diversity of S. argus distributed in Vietnam are still lacking. Therefore, mitochondrial cytochrome c oxidase subunit I (COI) gene was utilized to distinguish different populations and investigate the genetic diversity of two populations of S. argus from Tam Giang lagoon, Thua Thien Hue province (n = 31) and Ca Mau province (n = 14). The sequencing results indicated 13 distinct haplotypes among 45 sequences. Five single nucleotide polymorphisms were observed to distinguish Hue spotted scat population. The S. argus population in Ca Mau province was higher haplotype diversity (Hd) and nucleotide diversity (π) than those of Thua Thien Hue province, which demonstrates that there are minor differences between haplotypes. There were genetic distances ranging from 0%-4% within the populations and 6.67% between the two populations. In addition to the sequencing, the comparison of morphology, biology, culture, and the growth rate was sufficient to distinguish the spotted scat S. argus in Thua Thien Hue from Ca Mau.

• Molecules and Cells
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• v.19 no.3
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• pp.391-397
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• 2005

Molecular identification techniques are used where morphological characters are not useful for distinguishing species that resemble each other closely. The example studied here is the Adoxophyes species complex, in which A. orana (Fischer von $R{\ddot{o}}sslerstamm$) is officially the only known Korean species in the genus Adoxophyes (Lepidoptera: Tortricidae). However there have been suspicions that at least two types of A. orana exist in Korea based on the distribution and range of the host, with A. orana attacking apples and peaches, and another Adoxophyes sp. attacking tea and pears. The latter is presumed to be A. honmai (Yasuda), but the two have remained confused because of their extreme morphological similarity, despite several Asian studies of pheromonal and morphological characteristics. To confirm the occurrence of an Adoxophyes species other than A. orana in Korea, we compared 940 bp of the mitochondrial cytochrome oxidase I (COI) gene from 16 samples of Adoxophyes and found that there is a second Adoxophyes species different from A. orana. Comparison of the different sequences to that of Japanese A. honmai confirmed that they belong to the latter. From the sequence difference between the two Korean species, we were able to develop new PCR primer sets that distinguish them. This molecular identification technique with no enzyme digestion or sequencing step is a convenient and rapid way of differentiating between species that are hard to distinguish morphologically.

• The Plant Pathology Journal
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• v.40 no.2
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• pp.171-191
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• 2024

Identification of Helicotylenchus species is very challenging due to phenotypic plasticity and existence of cryptic species complexes. Recently, the use of rDNA barcodes has proven to be useful for identification of Helicotylenchus. Molecular markers are a quick diagnostic tool and are crucial for discriminating related species and resolving cryptic species complexes within this speciose genus. However, DNA barcoding is not an error-free approach. The public databases appear to be marred by incorrect sequences, arising from sequencing errors, mislabeling, and misidentifications. Herein, we provide a comprehensive analysis of the newly obtained, and published DNA sequences of Helicotylenchus, revealing the potential faults in the available DNA barcodes. A total of 97 sequences (25 nearly full-length 18S-rRNA, 12 partial 28S-rRNA, 16 partial internal transcribed spacer [ITS]-rRNA, and 44 partial cytochrome c oxidase subunit I [COI] gene sequences) were newly obtained in the present study. Phylogenetic relationships between species are given as inferred from the analyses of 103 sequences of 18S-rRNA, 469 sequences of 28S-rRNA, 183 sequences of ITS-rRNA, and 63 sequences of COI. Remarks on suggested corrections of published accessions in GenBank database are given. Additionally, COI gene sequences of H. dihystera, H. asiaticus and the contentious H. microlobus are provided herein for the first time. Similar to rDNA gene analyses, the COI sequences support the genetic distinctness and validity of H. microlobus. DNA barcodes from type material are needed for resolving the taxonomic status of the unresolved taxonomic groups within the genus.

• International Journal of Industrial Entomology and Biomaterials
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• v.9 no.2
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• pp.155-165
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• 2004

In Korean Peninsula including neighboring islands and Japanese Islands identical firefly species or the species belonging to same genera occur together in both territories. These geographic firefly species, nonetheless, have never been subject to taxonomic consideration together until recently, lacking clear species status and phylogenetic relationships. A recent serial study of these fireflies using luciferase gene and/or portions of mitochondrial DNA sequences provided some insight into these populations in terms of validity of species name, phylogenetic relationships, and speciation event. In this article, thus, we have reviewed the recent progress on phylogenetic and/or population genetic aspects of these species, i.e., Hotaria-group fireflies, Luciola lateralis, and Pyrocoelia rufa to better understand the firefly species in these regions.

• International Journal of Industrial Entomology and Biomaterials
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• v.15 no.1
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• pp.47-58
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• 2007

The tiny dragonfly, Nannophya pygmaea(Odonata: Libellulidae) is one the smallest dragonflies in the world and listed as a second-degree endangered wild animal and plant in Korea. For the long-term conservation of such endangered species, an investigation on nation-wide genetic magnitude and nature of genetic diversity is required as a part of conservation strategy. We, thus, sequenced a portion of mitochondrial COI gene, corresponding to "DNA Barcode" region(658 bp) from 68 N. pygmaea individuals collected over six habitats in Korea. The sequence data were used to investigate genetic diversity within populations and species, geographic variation within species, phylogeographic relationship among populations, and phylogenetic relationship among haplotypes. Phylogenetic analysis and uncorrected pairwise distance estimate showed overall low genetic diversity within species. Regionally, populations in southern localities such as Gangjin and Gokseong in Jeollanamdo Province showed somewhat higher genetic diversity estimates than those of remaining regions in Korean peninsula. Although geographic populations of N. pygmaea were subdivided into two groups, distance- or region-based geographic partition was not observed.

• Ocean and Polar Research
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• v.42 no.3
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• pp.263-270
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• 2020

The distribution and genotypes of the sea nettle Chrysaora pacifica have been reported in the South Sea of Korea; however, little research work has been attempted in the East Sea. Here, we collected similar jellyfishes from the East Sea coasts (Goseong, Yangyang and Sokcho), and identified them to the sea nettle morphologically. In addition, the genotypes of these sea nettle were compared with those from the South Sea (Tongyeong and Geoje). Phylogenetic analysis by using the mitochondrial COI sequences showed that the genus Chrysaora was clearly separated from other taxa to be formed a monophyletic group, with each species distinctly separated. C. pacifica in the East and South Seas was separated geographically by the COI phylogeography, representing potentially different populations. The COI gene of the Korean C. pacifica had approximately 7 times more genetic variation than the nuclear ITS rDNA, and thus it might be considered as a useful marker for genetic analysis of the jellyfish population.

• ALGAE
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• v.37 no.2
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• pp.135-147
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• 2022

The red algal genus Chondrus have long been used as raw materials for carrageenan and dietary fiber in health foods. Despite the importance of genetic information in safeguarding natural seaweed resources, knowledge of the population genetics of Chondrus in the northwest Pacific is limited. In this study, genetic diversity and phylogeographic structure of 45 populations (777 specimens) of Chondrus from Korea, China, and Japan were evaluated based on mitochondrial COI-5P gene sequences, and phylogenetic relationships were confirmed based on plastid rbcL gene sequences. Molecular analyses assigned the specimens in this study to three Chondrus species: C. nipponicus, C. ocellatus, and C. giganteus; phenotype-based species classification was impossible owing to their high morphological plasticity. We found moderate intraspecific genetic diversity and a shallow phylogeographic structure in both for C. nipponicus and C. ocellatus, and low intraspecific genetic diversity in C. giganteus. Each of the three species exhibited high-level intraspecific gene flow among regions based on the most common haplotypes (CN1 for C. nipponicus, CO1 for C. ocellatus, and CG1 for C. giganteus). Our comprehensive genetic information provides insights into the phylogeographic patterns and intraspecific diversity of the economically important Chondrus species. It also highlights the need to conserve existing natural Chondrus resources through continuous monitoring of genetic diversity and phylogeographic pattern.