• Korean Journal of Fisheries and Aquatic Sciences
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• v.49 no.6
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• pp.867-874
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• 2016

Although shrimps belonging to family Crangonidae are known to be genetically divergent and ecologically important among the various benthos, any of their mitochondrial genome has not been reported yet. We here determined the complete mitochondrial genome sequence of Crangon hakodatei (Rathbun, 1902), which was collected from East China Sea ($124^{\circ}E$ and $34.5^{\circ}N$). Total mitochondrial genome length of C. hakodatei was 16,060 bp, in which 13 proteins, 2 ribosomal RNAs, 22 transfer RNAs and a putative control region were encoded. Secondary structure prediction analysis showed that twenty tRNA genes exhibit the conserved structure but two genes, $tRNA^{Cys}$ and $tRNA^{Ser}$ (AGN), lack T and D arm, respectively. Based on the sequence similarity of the COI region from the currently reported five species belonging to genus Crangonidae, C. hakodatei was most closely related to Crangon crangon. Phylogenetic analysis of full COXI genes belonging to infraorder Caridea showed that only crangonid shrimps were clustered together with those of Dendrobranchiata. Gene order were well conserved from Penaeoidea to Caridea but $tRNA^{Pro}$ and $tRNA^{Thr}$ in Palaemonid shrimp were flipped each other by the recombination. Further study about mitochondrial genome sequences of shrimps belonging to Crangonidae should be made to know better about their evolutional relationships with other those in infraorder Caridea.

• International Journal of Industrial Entomology and Biomaterials
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• v.44 no.2
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• pp.55-64
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• 2022

Bombyx shini Park & Sohn, 2002 (Lepidoptera: Bombycidae), which was listed as an endemic species in South Korea has recently been renamed as the East Asian silk moth Rotunda rotundapex Miyata & Kishida, 1990 (Lepidoptera: Bombycidae). In this study, we sequenced the complete mitochondrial genome (mitogenome) of the R. rotundapex to announce genomic characteristics and to clarify its validity with a new name. The 15,294-bp long complete mitogenome comprises a typical set of genes [13 protein-coding genes (PCGs), 2 rRNA genes, and 22 tRNA genes] and one major noncoding, A + T-rich region, with an arrangement identical to that observed in most lepidopteran mitogenomes. The A/T content of the whole mitogenome was 79.22%; however, it varied among the regions/genes as follows: A + T-rich region, 91.62%; srRNA, 84.67%; lrRNA, 83.01%; tRNAs, 81.43%; and PCGs, 77.46%. Phylogenetic analyses of 35 species in the Bombycoidea superfamily showed the sister relationship between the families Sphingidae and Bombycidae s. str., with the higher nodal support [bootstrap support (BS) = 78%]. The Saturniidae was placed as the sister to the two families, but the nodal support for this relationship was low (BS = 53%). Current R. rotundapex was placed together with previously reported con-species with the highest nodal support, forming a separate clade from Bombyx, validating that B. shini can have a new genus name, Rotunda. However, the Korean R. rotundapex showed a substantial sequence divergence at 5.28% to that originated from an individual of type locality Taiwan in 1,459-bp of COI sequences. Considering such a high sequence divergence an additional study, which includes morphological and DNA barcoding data from further extensive distributional range maybe is needed for further robust taxonomic conclusion.

• Journal of Ecology and Environment
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• v.36 no.4
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• pp.449-463
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• 2013

DNA barcoding is becoming a widely applied tool to accurately discriminate red algae. We tested the effectiveness of DNA barcoding for identification and discovery of Champia species in Korea and clarified the phylogenetic relationships using the plastid rbcL gene. As results, we described four species of Champia such as C. inkyua sp. nov., C. recta Noda, C. bifida Okamura, and C. expansa Yendo. A new species, C. inkyua, is characterized by entangled thallus, terete and irregular branches, hooked apices, and longitudinal filaments running throughout the frond periphery only. Longitudinal filaments were composed of a complete cell with two half cells between diaphragms in the cavity. C. recta and C. bifida were reinstated with previously used names of C. parvula and C. compressa, respectively. C. recta is the first recorded species from Korea and is characterized by an erect thallus, terete and irregular branches, and straight apices. C. bifida is characterized by compressed thallus, pinnate or alternate branches, and bifid apices. C. expansa is characterized by flabellate thallus and dichotomous branches. Molecular analyses of COI and rbcL genes revealed sufficient sequence divergence to warrant species recognition in the genus Champia.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.49 no.4
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• pp.493-498
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• 2016

Squalus acanthias has been considered the valid scientific name for piked dogfish by many taxonomists, although others recognize two valid species, Squalus suckleyi and S. acanthias, based on differences in the numbers of precaudal vertebrae and their distribution. We compared Korean piked dogfish with S. acanthias from New Zealand using morphological and molecular methods to elucidate the taxonomy. The Korean piked dogfish was distinguished from S. acanthias from New Zealand by the number of precaudal vertebrae (70-75 in the former vs. 77-80 in the latter) and 540 base pairs in the mitochondrial DNA cytochrome c oxidase subunit I sequence (genetic distance: 0.007-0.013). Therefore, we suggest that the scientific name of the Korean piked dogfish be changed from S. acanthias to S. suckleyi.

• Fisheries and Aquatic Sciences
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• v.20 no.10
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• pp.26.1-26.9
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• 2017

Fishes in genus Sardinella are small pelagic species, which plays an important role in marine ecosystem as the first consumer. Those species are also commercially important, whose total catch reaches 278,600 tons in 2011 in Indonesia, but their identification has been difficult for their morphological similarity. In this study, we reported Sardinella jussieu for the first time in Indonesian coastal area (Banten Bay, Indonesia, $6^{\circ}\;0^{\prime}\;50.00^{{\prime}{\prime}}\;S-106^{\circ}\;10^{\prime}\;21.00^{{\prime}{\prime}}\;E$). We were able to confirm the species by both its morphological characteristics including the black spot at dorsal fin origin, the dusky pigmentation at caudal fin, 31 total scute numbers, and DNA sequence identity in the GenBank database by the molecular analysis. Its total mitochondrial genome was determined by the combination of next-generation sequencing and typical PCR strategy. The total mitochondrial genome of Sardinella jussieu (16,695 bp) encoded 13 proteins, 2 ribosomal RNAs, 22 transfer RNAs, and the putative control region. All protein-coding genes started with ATG and typical stop codon and ended with TAA or TAG except for ND4 in which AGA is used. Phylogenetic analyses of both COI region and full mitochondrial genome showed that S. jussieu is most closely related to Sardinella albella and Sardinella gibbosa

• Journal of Species Research
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• v.3 no.1
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• pp.7-16
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• 2014

Many species of Lymantria are important forestry pests, including L. dispar which is well known distributed from Asia to North America as an invasive species. Like of most other genera of moths, the systematic of this genus is still in dispute, especially on the monophyly and the relationship within this genus due to the fact that genus is very large and varied. This genus was morphologically defined only by a single aphomorphy. To clarify the monophyly of the genus Lymantria, to reveal the phylogenetic relationship among the Indonesian species, and to establish the genetic characters of Indonesian Lymantria, we analyzed 9 species of Indonesian Lymantria involving 33 other species distributed around the world based on nucleotide sequence variation across a 516-bp region in the CO I gene. The results showed that the base composition of this region was a high A+T biased (C: 0.3333). The results also showed that the monophyly of Lymantria was not supported by bootstrap tests at any tree building methods. Indonesian species was distributed into four different groups but the relationship among them was still in dispute. It indicates that relationships among the basal nodes (groups) proposed here were least valid due to the fact that the number of species may not be enough to represent the real number of species in the nature. Moreover CO I gene sequences alone were not able to resolve their relationships at the basal nodes. More investigations were needed by including more species and other genes that the more conserved.

• ALGAE
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• v.34 no.2
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• pp.91-97
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• 2019

Chilean species of marine macroalgae with amphitropical distributions oftentimes result from introductions out of the Northern Hemisphere. This possibility was investigated using haplotype data in an amphitropical red macroalgae present in Chile, Callophyllis variegata. Published sequence records from Canada and the United States were supplemented with new collections from Chile (April 2014-November 2015). Specimens of C. variegata were amplified for the 5′ end of the cytochrome c oxidase subunit I gene (COI-5P) and the full length nuclear internal transcribed spacer region. Haplotype networks and biogeographic distributions were used to infer whether C. variegata was introduced between hemispheres, and several population parameters were estimated using IMa2 analyses. C. variegata displayed a natural amphitropical distribution, with an isolation time of approximately 938 ka between hemispheres. It is hypothesized that contemporary populations of C. variegata were established from a refugial population during the late Pleistocene, and may have crossed the tropics via rafting on buoyant species of kelp or along deep-water refugia coincident with global cooling, representing a rare case of a non-human mediated amphitropical distribution.

• Korean journal of applied entomology
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• v.53 no.3
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• pp.281-286
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• 2014

In grape vineyards, whitish spots in a cloud shape have been often observed on the fruit surface recently. However, the cause of the halo spot symptom was unknown, hindering countermeasures to be properly designed for the control. A small hole in the middle of the formless halo spot remained as a scar formed by oviposition of the thrips. It became later a suberized scab, which is separated from the epidermal cells on the surface either to be retained on or to be detached from it as time proceeds. Such a symptom is distinguished from the feeding damages caused by thrips or true bugs occurring on the grape fruits. With DNA extracted from the egg-shell found in the hole, molecular diagnosis by amplifying an ITS2 region with universal primers and subsequently digesting the PCR product by an restriction enzyme (RsaI) revealed that the egg was laid by Frankliniella occidentalis. In addition, a mitochondrial COI sequence confirmed that the halo spot symptom was formed by its oviposition. This study provides accurate information on the peculiar damage symptom caused by oviposition of F. occidentalis that could be useful in the control strategies for this pest in vineyards.

• Korean journal of applied entomology
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• v.55 no.4
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• pp.471-475
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• 2016

The dark-winged fungus gnats are one of the most serious fly pests attacking the mushroom cultivation in Korea. They cause severe damage to the artificial sawdust beds used to cultivate mushroom, and reduce the production of button mushroom, Agaricus bisporus, in greenhouses. In this study, we collected nine species of the mushroom flies in order to identify the dominant species of the dark-winged fungus gnat attacking the A. bisporus plantation using the yellow sticky trap in Buyeo-gun, Boryeong-gun, Yongin-si and Chilgok-gun from April to June 2015. The collected samples were used to determine the DNA sequence of the cytochrome c oxidase subunit I (COI) of the nine different species by DNA barcoding. The sequencing results showed that Lycoriella ingenua was the dominant dark-winged fungus gnat species destroying A. bisporus cultivated on the artificial sawdust beds in Korea.

• Korean Journal of Environmental Biology
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• v.36 no.3
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• pp.352-358
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• 2018

This study aimed to develop a species identification method for the egg and fry of the three Korean bitterling fishes (Pisces: Acheilognathinae), including Acheilognathus signifer, Acheilognathus yamatsutae and Rhodeus uyekii based on the PCR-based Restriction Fragment Length Polymorphism (RFLP) markers. We conducted a field survey on the Deokchicheon River from the North Han River basin, where the three Acheilognathinae species co-occur, and also analyzed the existing sequence dataset available from the GenBank. We found coexistence of the three species at the study site. The egg and fry were obtained from the host mussels (Unio douglasiae sinuolatus) by hand from May to June 2015 and in May 2017. To develop PCR-based RFLP markers for species identification of the three Acheilognathinae fish species, restriction enzymes pinpointing species-specific single nucleotide variation (SNV) sites in mitochondrial DNA COI (cytochrome oxidase I) and cyt b (cytochrome b) genes were determined. Genomic DNA was extracted from the egg and fry and RFLP experiments were carried out using restriction enzymes Apal I, Stu I and EcoR V for A. signifer, A. yamatsutae and R. uyekii, respectively. Consequently, unambiguous discrimination of the three species was possible, as could be seen in DNA band patterns from gel electrophoresis. Our developed PCR-based RFLP markers will be useful for the determination of the three species for the young and would assist in studying the spawning patterns and reproductive ecology of Acheilognathinae fishes. Furthermore, we believe the obtained information will be of importance for future maintenance, management and conservation of these natural and endangered species.