• Korean Journal of Ichthyology
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• v.25 no.4
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• pp.222-226
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• 2013

As Carangoides ferdau was previously reported based on its underwater photograph, morphological descriptions have been incomplete up to the presence in Korea. On the base of two samples collected at the coast of Jeju island, morphological characters of C. ferdau are described in detail. This species is characterized by having the forepart of second dorsal fin much prolonged, 7~8 transverse dark bands on body, and snout length almost equal to eye diameter. It is morphologically very similar to C. orthogroammus, but is easily distinguished in having transverse dark bands instead of yellow spot on the body of C. orthogroammus. Phylogenetic relationships based on the mitochondrial cytochrome b (1,141 base pairs) sequences shows that C. ferdau is closely related to C. orthogroammus, and C. dinema also has a sister group relationship with C. ablongus. Both genetic distances (p-distances) are 8.2%, respectively.

• Korean Journal of Ichthyology
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• v.21 no.4
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• pp.291-298
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• 2009

A molecular phylogenetic relationship inferred from mitochondrial cytochrome b gene sequence was developed based on analysis of Zacco species distributed in Korea as well as China, Japan and Taiwan. A maximum parsimony (MP) tree showed that Korean Z. temminckii and Z. koreanus formed a monophyletic clade, but the populations of Z. temminckii and Z. koreanus in the 'South Korean Subdistrict' region had genetic similarity with Japanese Z. temminckii. Korean Z. platypus had a closer relationship with Japanese members of the clade than with Chinese Z. platypus, which was more closely related to Opsariichthys uncirostris amurensis. The analysis of neighbor joining (NJ) tree may support a hypothesis that the clade of Z. platypus had genetically diverged from the common ancestor of Zacco species comprising Z. koreanus, Z. temminckii, Z. sieboldii and other species; thereafter a cladogenesis of Z. koreanus and Z. temmminckii had occurred from the ancestor of Z. sieboldii. Moreover, the Chinese Z. platypus had diverged far from the Korean Z. platypus and formed a phylogenetic relationship with O. uncirostris amurensis. Therefore, a more detailed study of the taxonomy and systematics of Zacco species in regard to their zoogeographical distributions is needed.

• Journal of Aquaculture
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• v.21 no.3
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• pp.139-145
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• 2008

Morphological classification of echinoid species has many difficulties because of their phenotypic variations. In the present study, we analyzed morphotypes and partial mitochondrial 12S rDNA sequences of four sea urchin species classified as Pseudocentrotus depressus, Anthocidaris crassispina, Hemicentrotus pulcherrimus and Strongylocentrotus nudus, and unidentified four species collected from the coasts of the East sea. Their genomic DNAs were extracted from gonads and mitochondrial 12S rDNA sequences were amplified by the polymerase chain reaction (PCR) method. The sequence identities among the known four sea urchin species were 87.4-95.6%. The sequence identities among the unidentified four species were 99.4-99.6% and showed the highest homology to S. intermedius(99.8%). Thus, our phylogenetic tree indicates that the unidentified four species belong to S. intermedius.

• Korean Journal of Plant Taxonomy
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• v.40 no.4
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• pp.234-239
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• 2010

The taxonomy of umbel genus Sium L., Apiaceae in Korea was reviewed on the basis of molecular phylogenies derived from sequences of nuclear ribosomal DNA internal transcribed spacer (ITS) regions. The ITS sequence-derived phylogeny indicates that S. heterophyllum, endemic to Korea, is identical to S. tenue, which is known as endemic to Ussuri regions. Comparisons of sequence pairs across both spacer regions gave divergence values and revealed the identity between S. tenue and S. heterophyllum on Mt. Moonsoo. On the other hand, the ITS sequences support species delimitation of S. ternifolium, as reported recently as a new species that differs from other Sium species. The ITS sequence divergence values of 1.4 and 1.6% support species delimitation between S. serra and S. ternifolium.

• Korean journal of applied entomology
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• v.53 no.3
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• pp.247-260
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• 2014

To identify the species of Trichogramma occurring in the corn fields of Korea as egg parasitoids of Ostrinia furnacalis, we sequenced the full-length of ITS2 nuclear rDNA from 112 parasitoids collected during this study. As a reference to distinguish species, we also retrieved full-length ITS2 sequences of 60 Trichogramma species from the NCBI GenBank database. On the basis of the size and 3'terminal sequence pattern of the ITS2 sequences, the Trichogramma samples collected in this study were divided into three groups (K-1, -2, and -3). Evolutionary distances (d) within and between groups based on ITS2 sequences were estimated to be ${\leq}0.005$ and ${\geq}0.080$, respectively. In the net average distance between groups or species, the d value between K-1 and T. ostriniae, K-2 and T. dendrolimi, and K-3 and T. confusum was the lowest, with values of 0.016, 0.001, and 0.002, respectively. In the phylogenetic tree, K-1 and K-2 were clustered with T. ostriniae and T. dendrolimi, respectively. However, K-3 was clustered with three different species, namely, T. confusum, T. chilonis, and T. bilingensis. NCBI BLAST results revealed that parasitoids belonging to K-1 and K-2 showed 99% identity with T. ostriniae and T. dendrolimi, respectively. Parasitoids in K-3 collected from Hongcheon showed 99-100% identity with T. confusum and T. chilonis, and one parasitoid in K-3 collected from Gochang had 98% identity with T. bilingensis, T. confusum, and T. chilonis. On the basis of these results, we infer that the species of Trichogramma collected in this study are closely related to T. ostriniae (K-1) and T. dendrolimi (K-2). However, it was not possible to distinguish species of K-3 using the ITS2 sequence alone.

• Korean journal of applied entomology
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• v.56 no.4
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• pp.377-385
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• 2017

Estimates of evolutionary sequence divergence and inference of a phylogenetic tree for eight delphacid planthopper species were based on the full-length nucleotide sequence of the internal transcribed spacer 2 (ITS2) region. Size of the ITS2 DNA sequence varied from 550 bp in Sogatella furcifera to 699 bp in Nilaparvata muiri. Nucleotide sequence distance ($d{\pm}S.E.$) was lowest between N. muiri and N. bakeri ($0.001{\pm}0.001$), and highest between Ecdelphax cervina and Stenocranus matsumurai ($0.579{\pm}0.021$). Sequence distance between N. lugens and other planthoppers ranged from $0.056{\pm}0.008$ (N. muiri) to $0.548{\pm}0.021$ (S. matsumurai). In the neighbor-joining phylogenetic tree, all planthoppers were clustered separately into a species group, except N. muiri and N. bakeri. The ITS2 nucleotide sequence of N. lugens was used to design four loop-mediated isothermal amplification (LAMP) primer sets (BPH-38, BPH-38-1, BPH-207, and BPH-92) for N. lugens species-specific detection. After the LAMP reaction of three rice planthoppers, N. lugens, S. furcifera, and Laodelphax striatellus, with the four LAMP primer sets for 60 min at $65^{\circ}C$, LAMP products were observed in the genomic DNA of N. lugens only. In the BPH-92 LAMP primer set, the fluorescence relative to that of the negative control differed according to the amount of DNA (0.1 ng, 10 ng, and 100 ng) and incubation duration (20 min, 30 min, 40 min, and 60 min). At $65^{\circ}C$ incubation, the difference was clearly observed after 40 min with 10 ng and100 ng, but with a 60-min incubation period, the minimum DNA needed was 0.1 ng. However, there was little difference in fluorescence among all DNA amounts tested with 20 or 30 min incubations.

• Korean Journal of Plant Taxonomy
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• v.40 no.1
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• pp.1-15
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• 2010

Recognizing a basal group in a taxon is one of the most important factors involved in understanding the evolutionary history of that group of life. Many botanists have suggested a sister to all other angiosperms to understand the origin and rapid diversification of angiosperms based on morphological and fossil evidence. Recent technical advances in molecular biology and the accumulation of molecular phylogenetic data have provided evidence of the extant basal-most angiosperm which is a sister to all other angiosperms. Although it is still arguable, most plant taxonomists agree that Amborella trichopoda Baill., a species (monotypic genus and monotypic family) distributed in New Caledonia, is a sister to all other extant angiosperms based on evidence from the following molecular approaches: 1) classical phylogenetic analyses based on multiple genes (or DNA regions), 2) analyses of a tree network of duplicated gene families, and 3) gene-structural evidence. As an alternative hypothesis with relatively minor evidence, some researchers have also suggested that Amborella and Nymphaeaceae form a clade that is a sister to all other angiosperms. Debate regarding the basal-most angiosperms is still ongoing and is currently one of the hot issues in plant evolutionary biology. We expect that sequencing of the whole genome of Amborella as an evolutionary model plant and subsequent studies based on this genome sequence will provide information regarding the origin and rapid diversification of angiosperms, which is Darwin's so called abominable mystery.

• The Sea:JOURNAL OF THE KOREAN SOCIETY OF OCEANOGRAPHY
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• v.24 no.2
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• pp.236-248
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• 2019

We investigated occurrence and molecular phylogeny of the toxic epiphytic dinoflagellate Ostreopsis at seven sampling sites in the coastal waters off Jeju Island of Korea in April, 2017. During the sampling period, surface water temperature ranged from 15.7 to $18.3^{\circ}C$ and salinity was relatively constant, ranging from 33.4 to 34.9. Of a total of 13 macroalgal species collected from all sampling sites, Ostreopsis cells were observed from 8 macroalgal species and the highest cell abundance ($157.5cells\;g^{-1}$) was recorded on the red alga Grateloupia filicina at St. 6. LSU rDNA D8/D10 sequences of all Korean Ostreopsis strains isolated from the 4 sampling sites were 100% identical. Molecular phylogentic analyses (BI and ML) inferred from LSU rDNA alignment showed that the Korean Ostreopsis strains placed into the previously described the Ostreopsis sp. 1 clade, which contained strains isolated from the temperate coastal waters of Japan. The Korean Ostreopsis sp. 1 strain grew in a wide range of temperature ($10-30^{\circ}C$) and salinity (25-30), with its maximum growth rate of $0.49d^{-1}$ at $25^{\circ}C$ and salinity of 30, indicating that they can be tolerated in temperate areas.

• Journal of Plant Biotechnology
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• v.49 no.1
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• pp.30-38
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• 2022

Solanum brevicaule is one of the tuber-bearing wild Solanum species. Because of its resistance to several important pathogens infecting potatoes during cultivation, it can be used for potato breeding. However, the fact that S. brevicaule used in this study has an EBN value of two causes the sexual reproduction barriers between the species and cultivated potatoes. In this study, specific markers for discriminating S. brevicaule from other Solanum species were developed on the basis of the results of sequence alignments with the whole chloroplast genomes of S. brevicaule and seven other Solanum species. The chloroplast genome of S. brevicaule was completed by next-generation sequencing technology described in other recent studies. The total sequence length of the chloroplast genome of S. brevicaule is 155,531 bp. Its structure and gene composition are similar to those of other Solanum species. Phylogenetic analysis revealed that S. brevicaule was closely grouped with other Solanum species. BLASTN search showed that its genome sequence had 99.99% and 99.89% identity with those of S. spegazzinii (MH021562) and S. kurtzianum (MH021495), respectively. Sequence alignment identified 27 SNPs that were specific to S. brevicaule. Thus, three PCR-based CAPS markers specific to S. brevicaule were developed on the basis of these SNPs. This study will facilitate in further studies on evolutionary and breeding aspects in Solanum species.

• Journal of Plant Biotechnology
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• v.49 no.3
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• pp.178-186
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• 2022

The tetraploid Solanum acaule is a wild potato species from Bolivia widely used for potato breeding because of its diverse attractive traits, including resistance to frost, late blight, potato virus X, potato virus Y, potato leafroll virus, potato spindle tuber viroid, and cyst nematode. However, the introgression of useful traits into cultivated potatoes via crossing has been limited by differences in endosperm balance number between species. Somatic fusion could be used to overcome sexual reproduction barriers and the development of molecular markers is essential to select proper fusion products. The chloroplast genome of S. acaule was sequenced using next-generation sequencing technology and specific markers for S. acaule were developed by comparing the obtained sequence with those of seven other Solanum species. The total length of the chloroplast genome is 155,570 bp, and 158 genes were annotated. Structure and gene content were very similar to other Solanum species and maximum likelihood phylogenetic analysis with 12 other species belonging to the Solanaceae family revealed that S. acaule is very closely related to other Solanum species. Sequence alignment with the chloroplast genome of seven other Solanum species revealed four InDels and 79 SNPs specific to S. acaule. Based on these InDel and SNP regions, one SCAR marker and one CAPS marker were developed to discriminate S. acaule from other Solanum species. These results will aid in exploring evolutionary aspects of Solanum species and accelerating potato breeding using S. acaule.