• 한국동물학회지
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• 제35권2호
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• pp.219-225
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• 1992

The genetic variation in mitochondrial DNA (mtDNA) was analysed within and between two species of tree frogs. Hyla japonica and H. suweonensis from South Korea. Purified mtDNAs were digested with each of 11 restriction enLvmes which cleave at six base recognition sequences. The genome size of H. iaponica revealed ho types (20.0 $\pm$ 0.3 and 19.6 $\pm$ 0.3 kb) and this difference is explained by either addition or deletion of about 0.4 kb fragment. On the other hand, the genome sire of H. suueonensis was about 19.0 $\pm$ 0.4 kb only. For the analysis, level of fragment homology (F) and nucleotide sequence divergence (p) were estimated from comparisons of digestion profiles. Among four populations of H. iaponica, substantial mean sequence divergence was 0.017 (range 0.001-0.026); between identical types, 0.001 IslilaRl type) and 0.004 (Large type) respectively; between different ones, 0.024 (range 0.023-0.026). The level of sequence divergence between he species was 0.142 (range 0.131-0.146). This result suggested that he species ㅂwere distinctly differentiated species. The divergence time between ko species was estimated 7.1 million years.

• International Journal of Industrial Entomology and Biomaterials
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• 제24권1호
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• pp.41-47
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• 2012

The Scarites aterrimus (Coleoptera: Carabidae) dwells exclusively on coastal sandy dunes. Previously, we investigated the nation-wide magnitude and nature of genetic diversity of the species using mitochondrial COI gene and found moderate to low magnitude of sequence diversity, the presence of closely related haplotypes, and relatively high gene flow estimate. Based on these observations we concluded that the species had no historical barriers that bolster genetic subdivision and possible population decline. In this study, we additionally sequenced mitochondrial COII gene from 23 individuals collected from 9 Korean localities to confirm previous findings. Sequencing of 688 bp COII gene provided 5 haplotypes ranging in sequence divergence from 0.145% to 0.291% (1 ~ 2 bp), further confirming low sequence divergence of the species. Gene flow estimates and genetic diversity estimates also support the previous findings that there had been no historical barriers that bolster genetic subdivision.

• 한국어류학회지
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• 제12권4호
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• pp.223-229
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• 2000

한국산 미꾸리과 어류의 계통유전학적 관계를 고찰하고자 8종의 mitochondrial cytochrome b의 유전자 서열을 비교한 결과 대부분 이전의 형태학적 연구의 결과와 일치하였다. 그러나 종개속 Orthrias과 쌀미꾸리속 Lefua의 분류학적 위치는 미꾸리과 Cobitidae와 paraphyletic group으로 나타났으며 이 두 속의 sequence divergence는 0.184~0.272으로 나타나 미꾸리과와 잉어과 사이의 divergence와 유사하였다. 한편 참종개속 Iksookimia 2종과 북방종개 Cobitis melanoleuca는 각각 다르게 분화한 결과를 보여 주었으며 또한 중국산 미꾸리와 한국산 영덕 미꾸리의 sequence divergence는 0.099로 종간의 divergence를 보여주어 주목되었다. 미꾸리과 어류 가운데 참종개속의 일부 어류는 분류학적 위치로 보아 이들의 기원이 미꾸리과의 속간 잡종기원으로 생각된다.

• Animal cells and systems
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• 제3권2호
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• pp.199-205
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• 1999

The nucleotide sequences of a 504 bp segment of the mitochondrial cytochrome b gene were analyzed to survey the intraspecific variation of the brown frog, Rana dybowskii, collected from nine populations in South Korea. Comparisons of sequence divergence of the cytochrome b gene suggest that the populations examined are clearly classified into two types (type 1 and type 2), diverged from each other by a high value of 14.3-15.9% sequence divergence. The two types are distributed allopatrically in most populations, but only one population occurs sympatrically. In the Tonghae population, their spawning grounds differ in that type 1 spawns in the puddle and type 2 spawns in the mountain creek. Based on the genetic divergences of the cytochrome b gene sequences, the phylogenetic status of Korean R. dybowskii is elucidated by comparing it with related brown frogs distributed in an area adjacent to the Korean Peninsula. Interspecific sequence divergences among type 1, type 2 and other related brown frog species (Russian R. dybowskii, R. pirica, R. ornativentris, R. chensinensis: 2n=24 chromosomes) used in this study ranged from 11.7 to 16.3%. R. dybowskii in Tsushima is very similar to our type 1 (sequence divergence＝0-1.6%) and R. chensinensis in western China is closest to our type 2 (sequence divergence＝6.8-7.5%).

• 한국컴퓨터정보학회논문지
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• 제10권5호
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• pp.1-10
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• 2005

다중 서열 정렬(multiple sequence alignment, MSA)은 단백질과 핵산 서열들의 분석에 필요한 가장 중요한 도구이다. 생물학적인 서열들은 그들 사이의 유사성과 차이점을 보여주기 위하여 각각의 서열들을 수직적으로 정렬한다. 본 논문에서는 클러스터링 분기를 이용하여 두 그룹의 서열들 사이에서 정렬을 수행하는 효율적인 그룹 정렬 방법을 제안하였다. 제안한 알고리즘(Multiple Sequence Alignment using Clustering Divergence : CDMS)은 하향식 발견 방법인 트리 형태의 병합을 위해 클러스터링 방법으로 구축하였다. 클러스터링 방법은 가장 긴 거리를 가지는 서열을 두 개의 클러스터로 나눌 수 있다는 것에 기초하였다. 제안한 새로운 서열 정렬 알고리즘은 기존의 Clustal W알고리즘 보다 질적 향상과 처리 시간 단축 O($n^{3} L^{2}$)이 기대된다.

• International Journal of Industrial Entomology and Biomaterials
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• 제23권1호
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• pp.155-166
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• 2011

The leaf beetle, $Chrysolina$ $aurichalcea$ (Coleoptera: Chysomelidae), is a pest damaging plants of Compositae. In order to understand the genetic diversity and geographic variation we sequenced a portion of mitochondrial COI gene (658 bp) and complete nuclear internal transcribed spacer 2 (ITS2) of the species collected from seven Korean localities. A total of 17 haplotypes (CACOI01~CACOI17), with the maximum sequence divergence of 3.04% (20 bp) were obtained from COI gene sequence, whereas 16 sequence types (ITS2CA01~ITS2CA16), with the maximum sequence divergence of 2.013% (9 bp) were obtained from ITS2, indicating substantially larger sequence divergence in COI gene sequence. Phylogenetically, the COI gene provided two haplotype groups with a high nodal support (${\geq}87%$), whereas ITS2 provided only one sequence type group with a high nodal support (${\geq}92%$). The result of COI gene sequence may suggest the presence of historical biogeographic barriers that bolstered genetic subdivision in the species. Different grouping pattern between COI gene and ITS2 sequences were interpreted in terms of recent dispersal, reflected in the ITS2 sequence. Finding of unique haplotypes and sequence types only from Beakryeng-Islet population was interpreted as an intact remnant of ancient polymorphism. As more samples are analyzed using further hyper-variable marker, further fruitful inference on the geographic contour of the species might be available.

• Animal cells and systems
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• 제4권3호
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• pp.267-272
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• 2000

Partial sequence of the mitochondrial cytochrome b gene was analyzed to investigate genetic variation from 10 geographic populations of Granulilittorina exigua in Korea. The sequence of 282 base pairs was determined by PCR-directed silver sequencing method. The sequences of two species within the genus Littorina reserved in NIH blast search were utilized to determine geographic variations of species referred. The levels of mtDNA sequence differences were 0.00-2.54% within populations and 0.71-4.43% between populations. There were four amino acid differences between representative species of the genera Granulilittorina and Littorina, but no differences within populations of the genus Granulilittorina. The UPGMA and the N-J trees based on Tamura-Nei genetic distance matrix were constructed, which showed that the genus Granulilittorina was divided into three groups such as eastern (even exception for Tokdo population), southern, and western regional populations. The degrees of genetic divergence within populations of each group were p=0.021, p=0.019, and p=0.018, respectively. The divergence between the eastern and southern populations was p=0.032, showing closer relationship than with the western populations (p=0.052). Based on the diverged time estimation, the eastern and southern populations of Granulilittorina exigua in Korea diverged from the western populations about 2.1 MYBP, and the eastern and southern populations diverged from each other about 1.3 MYBP.

• Molecules and Cells
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• 제27권3호
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• pp.365-381
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• 2009

The chloroplast DNA sequences of Megaleranthis saniculifolia, an endemic and monotypic endangered plant species, were completed in this study (GenBank FJ597983). The genome is 159,924 bp in length. It harbors a pair of IR regions consisting of 26,608 bp each. The lengths of the LSC and SSC regions are 88,326 bp and 18,382 bp, respectively. The structural organizations, gene and intron contents, gene orders, AT contents, codon usages, and transcription units of the Megaleranthis chloroplast genome are similar to those of typical land plant cp DNAs. However, the detailed features of Megaleranthis chloroplast genomes are substantially different from that of Ranunculus, which belongs to the same family, the Ranunculaceae. First, the Megaleranthis cp DNA was 4,797 bp longer than that of Ranunculus due to an expanded IR region into the SSC region and duplicated sequence elements in several spacer regions of the Megaleranthis cp genome. Second, the chloroplast genomes of Megaleranthis and Ranunculus evidence 5.6% sequence divergence in the coding regions, 8.9% sequence divergence in the intron regions, and 18.7% sequence divergence in the intergenic spacer regions, respectively. In both the coding and noncoding regions, average nucleotide substitution rates differed markedly, depending on the genome position. Our data strongly implicate the positional effects of the evolutionary modes of chloroplast genes. The genes evidencing higher levels of base substitutions also have higher incidences of indel mutations and low Ka/Ks ratios. A total of 54 simple sequence repeat loci were identified from the Megaleranthis cp genome. The existence of rich cp SSR loci in the Megaleranthis cp genome provides a rare opportunity to study the population genetic structures of this endangered species. Our phylogenetic trees based on the two independent markers, the nuclear ITS and chloroplast MatK sequences, strongly support the inclusion of the Megaleranthis to the Trollius. Therefore, our molecular trees support Ohwi's original treatment of Megaleranthis saniculifolia to Trollius chosenensis Ohwi.

• International Journal of Industrial Entomology and Biomaterials
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• 제26권2호
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• pp.95-112
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• 2013

As a first step toward understanding the divergence and relationships of the Nymphalidae (Lepidoptera: Papilionoidea) occurring in South Korea, cytochrome oxidase subunit I (COI), 16S ribosomal RNA (16S rRNA), and elongation factor-$1{\alpha}$ (EF-$1{\alpha}$) that comprise 3,501-3,716 bp were either sequenced (55 species) or the sequences were obtained from GenBank (23 species). The concatenated sequence divergence of six nymphalid subfamilies ranked in the following order: Danainae (10.3%), Satyrinae (9.5%), Limenitidinae (8.0%), Apaturinae (7.0%), Nymphalinae (6.7%), and Heliconiinae (6.2%). As has been reported in previous large scale international studies, the subfamilial relationships of (((((Limenitidinae + Heliconiinae) + (Nymphalinae + Apaturinae)) + Satyrinae) + Libytheinae) + Danainae) were also confirmed, except for the switched positions between Danainae and Libytheinae, and supported all subfamilies and tribe monophylies. Unlikely consistent phylogenetic relationships among genera within the majority of tribes in Nymphalidae, a conflicting relationship within the subfamily Apaturinae was obvious, presenting Apatura as sister to either Mimathyma or (Mimathyma + (Sephisa + (Hestina + Sasakia))), and both of these relationships are unconventional. Within the subfamily Limenitidinae, the genus Neptis was consistently revealed as a paraphyletic with respect to the genus Aldania, requiring further taxonomic investigation of the genus. Although limited, current sequence information and phylogenetic relationships are expected to be helpful for further studies.

• International Journal of Industrial Entomology and Biomaterials
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• 제14권2호
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• pp.107-112
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• 2007

The mole crickets, Gryllotalpa, are insect pest distributed in the world. In Korea, G. orientalis was reported to occur, but previous ecological studies suggested the presence of two ecological types. To test this hypothesis, we sequenced a portion of mitochondrial (mt) genome from 48 G. orientali individuals collected over five Korean localities: Busan, Suwon, Okchon, Wonju, and Gangneung. From the sequence analysis, only two haplotypes were obtained, but the sequence divergence between the two haplotypes was 11 %, suggesting the presence of two distinct genetic groups in Korea. Although the population of Busan, Okchon, Wonju, and Gangneung was identified as a single haplotype, but that of Suwon was occupied by both hapotypes. Considering sequence divergence of other insect species occurring in Korea, the divergence estimate found between the two haplotypes seems to be too large to be considered as identical species. This result may suggest that the two differentiated haplotypes found in this study may reflect the previously reported two ecological types found in Suwon, Korea. To further understand the genetic divergence of the two phylogenetic groups, analysis of more variable regions of G. orientalis genome is required.