• BMB Reports
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• v.31 no.6
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• pp.604-606
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• 1998

The nucleotide sequence of two hypervariable regions of the D-loop and the frequency of the 9-bp repeat in the region V of mitochondrial DNA (mtDNA) were investigated in the Korean population. Alignment of these sequences with the published reference revealed a unique pattern of base substitution and deletion compared with those of other races. The deletion and addition frequency of the 9-bp repeat in the region V was also distinct.

• Animal cells and systems
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• v.3 no.4
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• pp.393-397
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• 1999

Length variations in human mitochondrial DNA (mtDNA) offer useful markers in the study of female aspects of human population history. One such length variation is a 9-bp deletion in the small noncoding segment located between the COII and Iysine tRNA genes (COII/tRNA/$^{Lys}$ intergenic region) which usually contain two tandemly arranged copies of a 9-bp sequence (ccccctcta) in human mtDNA. The mtDNA 9-bp deletion and polymorphic variants of expanded 9-bp repeat motif in the intergenic COII/tRNA$^{Lys}$ region have been found at varying frequencies among different human ethnic groups. We have examined the length variation of the mtDNA COII/tRNA$^{Lys}$ intergenic region from a total of 813 individuals in east Asian populations. The occurrence of the 9-bp deletion was found to be relatively homogeneous in northeast Asian populations (Chinese, 14.2%; Japanese, 14.3%: Koreans, 15.5%), with the exception of Mongolians (5.1%). In contrast, Indonesians (25.0%) and Vietnamese (23.2%) of the southeast Asian populations appeared to have relatively high frequencies of the 9-bp deletion. We identified the existence of a new expanded 9-bp repeat motif which likely resulted from a slipped mispairing insertion of six more cytosines in the intergenic COII$^{Lys}$ region. It was present at low frequencies in the Korean (2/349) and Japanese populations (2/147). Based on the results of this study, the Korean population may reflect a close genetic affinity with the Japanese and Chinese populations than the others surveyed east Asian populations.

• Journal of the Korean Academy of Child and Adolescent Psychiatry
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• v.16 no.2
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• pp.199-210
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• 2005

Objective : Attention deficit hyperactivity disorder(ADHD) affects $5-10\%$ of children in Korea, with more boys and girls being diagnosed. Despite seriousness of ADHD, little is known about its causes. From the current genetic epidemiologic studies, ADHD is known as a heritable disorder. Till now, however, there have been very few genetic studies about ADHD in Korea. The aim of the this study is to examine the association between dopamine transporter gone type 1 and ADHD using case-control design in Korean ADHD probands and normal controls. Materials and Method : Child Psychiatric Genetic research team in Seoul National University Hospital, Clinical Research Institute recruited the ADHD probands using clinical interview/observation, diverse rating scales, and neuropsychological tests. For eliminating phenocopy or ADHD, diagnosis of ADHD was based upon clinical data, psychometric data, and parent/teacher reports. Total 85 ADHD-probands were recruited as final study subjects and independent 100 normal adults participated in this study as control group. For all the ADHD probands, and controls, the 3'-UTR-VNTR polymorphism of DAT1 was analyzed. Based on the DAT1 allele and genotype informations, Chi-square test based on case-control design was performed. Results : As for genetic study, total of 85 probands and 100 controls were included for the genetic analysis. Four different alleles, 350bp (7repeat), 440bp (9repeat), 480bp (10repeat) and 520bp (11repeat) were found in DAT1 gene of study subjects. In case-control analysis, ADHD probands and parents have significantly more 9 repeat allele and 9/10 genotype. Also, The probands with 9repeat allele have more commission errors in ADS. Conclusion : The positive association between ADHD and DAT1 gene was replicated in this report like other previous results for caucasian children and Korean children with ADHD. There are ongoing studies on other candidate genes such as DRD4 and DRD5 and it would be required to explore the association of these candidate genes in Korean children with ADHD. These ongoing genetic research will contribute to the understanding of heterogenous genetic and environmental etiologies of ADHD phenotype, which will lead to the development of more comprehensive treatment and preventive interventions for ADHD.

• Korean Journal of Plant Resources
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• v.32 no.6
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• pp.644-668
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• 2019

Dysphania ambrosioides (L.) Mosyakin & Clemants which belongs to Chenopodiaceae/Amaranthaceae sensu in APG system has been known as a useful plant in various fields as well as an invasive species spreading all over the world. To understand its phylogenetic relationship with neighbour species, we completed chloroplast genome of D. ambrosioides collected in Korea. Its length is 151,689 bp consisting of four sub-regions: 83,421 bp of large single copy (LSC) and 18,062 bp of small single copy (SSC) regions are separated by 25,103 bp of inverted repeat (IR) regions. 128 genes (84 protein-coding genes, eight rRNAs, and 36 tRNAs) were annotated. The overall GC content of the chloroplast genome is 36.9% and those in the LSC, SSC and IR regions are 34.9%, 30.3%, and 42.7%, respectively. Distribution of simple sequence repeats are similar to those of the other two Dysphania chloroplasts; however, different features can be utilized for population genetics. Nucleotide diversity of Dysphania chloroplast genomes 18 genes including two ribosomal RNAs contains high nucleotide diversity peaks, which may be genus or species-specific manner. Phylogenetic tree presents that D. ambrosioides occupied a basal position in genus Dysphania and phylogenetic relation of tribe level is presented clearly with complete chloroplast genomes.

• Korean Journal of Plant Taxonomy
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• v.51 no.3
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• pp.337-344
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• 2021

The chloroplast genome of Limonium tetragonum (Thunb.) Bullock, a halophytic species, was sequenced to understand genetic differences based on its geographical distribution. The cp genome of L. tetragonum was 154,689 bp long (GC ratio is 37.0%) and has four subregions: 84,572 bp of large single-copy (35.3%) and 12,813 bp of small single-copy (31.5%) regions were separated by 28,562 bp of inverted repeat (40.9%) regions. It contained 128 genes (83 protein-coding genes, eight rRNAs, and 37 tRNAs). Thirty-five single-nucleotide polymorphisms and 33 INDEL regions (88 bp in length) were identified. Maximum-likelihood and Bayesian inference phylogenetic trees showed that L. tetragonum formed a sister group with L. aureum, which is incongruent with certain previous studies, including a phylogenetic analysis.

• Korean Journal of Plant Taxonomy
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• v.52 no.3
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• pp.156-172
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• 2022

Campsis grandiflora (Thunb.) K. Schum is an ornamental species with various useful biological effects. The chloroplast genome of C. grandiflora isolated in Korea is 154,293 bp long (GC ratio: 38.1%) and has four subregions: 84,121 bp of large single-copy (36.2%) and 18,521 bp of small single-copy (30.0%) regions are separated by 24,332 bp of inverted repeat (42.9%) regions including 132 genes (87 protein-coding genes, eight rRNAs, and 37 tRNAs). One single-nucleotide polymorphism and five insertion and deletion (INDEL) regions (40-bp in total) were identified, indicating a low level of intraspecific variation in the chloroplast genome. All five INDEL regions were linked to the repetitive sequences. Seventy-two normal simple sequence repeats (SSRs) and 47 extended SSRs were identified to develop molecular markers. The phylogenetic trees of 29 representative Bignoniaceae chloroplast genomes indicate that the tribe-level phylogenic relationship is congruent with the findings of previous studies.

• Animal cells and systems
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• v.2 no.2
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• pp.259-267
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• 1998

A deletion of one out of the two copies of 9-bp repeat sequence (CCCCCTCTA), between the cytochrome oxidase II and Iysine tranfer RNA (COII/$tRNA^{Lys}$) genes in human mitochondrial DNA (mtDNA) has been used as a polymorphic anthropological marker for people of east Asian origin, and to lesser extent, Pacific and African populations. We searched for the 9-bp deletion of the intergenic COII/$tRNA^{Lys}$ Lys region in two Korean populations (175 from Seoul and 38 from Cheju) and examine the distibution of this deletion in world populations. The 9-bp deletion was detected directly by electrophoresis of the polymerase chain reaction (PCR)-amplified nucleotide(nt) 8211-8310 mtDNA fragment. The frequencies of the 9-bp deletion were significantly different between the Seoul (16%) and Cheju (8%) populations. Examination of data from the world populations suggests a geographic gradient. The frequency reaches its highest values in some Pacific island populations and decreases along the southeast Asia-Siberia transect. In spite of this geographic gradient, Mongoloid populations including Korean, Chinese, Japanese, and Mongolian populations were relatively homo-geneous with regard to the 9-bp deletion type of the intergenic COII/$tRNA^{Lys}$ region. These results indicate Koreans are genetically related to northeast Asian populations, and have a maternal mongoloid ancestry. Therefore, the 9-bp deletion of the intergenic COII/$tRNA^{Lys}$ region will provide significant information to elucidate the historical patterns of migration of the Mongoloids.

• Korean Journal of Plant Taxonomy
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• v.51 no.2
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• pp.171-175
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• 2021

Daphne genkwa (Thymelaeaceae) is a small deciduous shrub widely cultivated as an ornamental. The complete chloroplast genome of this species is presented here. The genome is 132,741 bp long and has four subregions: 85,668 bp of large single-copy and 28,365 bp of small single-copy regions are separated by 9,354 bp of inverted repeat regions with 107 genes (71 protein-coding genes, four rRNAs, and 31 tRNAs) and one pseudogene. The phylogenetic tree shows that D. genkwa is nested within Wikstroemia and is not closely related to other species of Daphne, suggesting that it should be recognized as a species of Wikstroemia.

• Molecules and Cells
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• v.27 no.3
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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.

• Asian-Australasian Journal of Animal Sciences
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• v.20 no.3
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• pp.313-315
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• 2007

Seventeen haplotypes were detected from the complete mitochondrial DNA control region sequences analyzed from eighty individuals of two Tibetan domestic sheep breeds. The nucleotide composition of all the sequences was 33.0% A, 29.7%T, 22.9%C and 14.4%G; G+C was 37.3%. The length of the sequences ranged from 1,107 bp to 1,259 bp. The difference between them was primarily due to 3-5 copy numbers of a 75 bp tandem repeat sequence. The NJ phylogenetic tree (the number of replications of bootstrap test is 1,000) presented three major domestic sheep lineages, which suggested that modern Tibetan sheep breeds are derived from three maternal sources.