• Proceedings of the Plant Resources Society of Korea Conference
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• 2020.12a
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• pp.55-55
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• 2020

뫼제비꽃(Viola selkirkii)의 엽록체 DNA 염기서열을 차세대염기서열분석법(NGS)을 이용하여 분석하였다. 재료는 강원도 화천군 일산과 제주도 한라산의 2개체를 사용하였다. 분석결과, 염기서열의 길이는 일산의 뫼제비꽃이 156,774 bp (GC content: 36.30%), 한라산의 뫼제비꽃이 157,451 bp(GC content: 36.30%)로 한라산 개체가 길게 분석되었다. 구간별로 LSC(Large single copy)지역은 한라산 개체(85,950 bp)가 일산 개체(85,930 bp)보다 20 bp 길었으며, SSC(Small single copy)지역은 한라산 개체(17,261 bp)보다 일산 개체가 17,982 bp로 길게 분석되었다. IR(Inverted repeat)지역은 한라산 개체가 27,120 bp로 일산 개체(26,431 bp)보다 길게 분석되었다. 이러한 염기서열 길이의 차이는 종내 개체 간 빈번하게 발생하는 현상으로 IGS와 intron 구간에서 확인 된 단순반복서열의 일부 누락과 IR지역 내의 수축과 확장에 의한 것으로 판단된다. 뫼제비꽃 2개체의 엽록체 게놈을 구성하는 유전자 수는 총 111개로 동일하였으며, protein coding gene 77개, tRNA(transfer RNA) gene 30개, 그리고 rRNA (ribosomal RNA) gene 4개로 구성되어 있었다. 이는 기 발표된 엽록체 DNA 전체 염기서열이 밝혀진 제비꽃속 (Viola) 종류들과 동일한 결과이다.

• Journal of Gastric Cancer
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• v.4 no.2
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• pp.109-120
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• 2004

Purpose: Individual gastric cancers demonstrate complicated genetic alterations. The PCR-based analysis of polymorphic microsatellite sequences on cancer-related chromosomes has been used to detect chromosomal loss and microsatellite instability. For the purpose of preoperative usage, we analyzed the correspondance rate of the microsatellite genotype between endoscopic biopsy and surgical specimens. Materials and Methods: Seventy-three pairs of biopsy and surgical specimens were examined for loss of heterozygosity and microsatellite instability by using 40 microsatellite markers on eight chromosomes. Microsatellite alterations in tumor DNAs were classified into a high-risk group (baselinelevel loss of heterozygosity: 1 chromosomal loss in diffuse type and high-level loss of heterozygosity: 4 or more chromosomal losses) and a low-risk group (microsatellite instability and low-level loss of heterozygosity: 2 or 3 chromosomal losses in diffuse type or $1\∼3$ chromosomal losses in intestinal type) based on the extent of chromosomal loss and microsatellite instability. Results: The chromosomal losses of the biopsy and the surgical specimens were found to be different in 21 of the 73 cases, 19 cases of which were categorized into a genotype group of similar extent. In 100 surgical specimens, the high-risk genotype group showed a high incidence of nodal involvement (19 of 23 cases: $\leq$5 cm; 23 of 24 cases: >5 cm) irrespective of tumor size while the incidence of nodal involvement for the low-risk genotype group depended on tumor size (5 of 26 cases: $\leq$5 cm; 18 of 27 cases: >5 cm). Extraserosal invasion was more frequent in large-sized tumor in both the high-risk genotype group ($\leq$5 cm: 12 of 23 cases; >5 cm: 23 of 24 cases) and the low-risk genotype group ($\leq$5 cm: 7 of 26 cases; >5 cm: 16 of 27 cases). The preoperative prediction of tumor invasion and nodal involvement based on tumor size and genotype corresponded closely to the pathologic tumor stage (ROC area >0.7). Conclusion: An endoscopic biopsy specimen of gastric cancer can be used to make a preoperative genetic diagnosis that accurately reflect the genotype of the corresponding surgical specimen.

• Journal of the Korean Society of International Agriculture
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• v.23 no.5
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• pp.546-551
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• 2011

Chrysanthemums, often called mums or chrysanths, belong to the genus Chrysanthemum, which includes about 30 species of perennial flowering plants in the family Asteraceae. We extracted DNA from Dendranthema grandiflorum ('Smileball') to construct a simple sequence repeat (SSR)-enriched library, using a modified biotin-streptavidin capture method. GS FLX (Genome Sequencer FLX System which provides the flexibility to perform the broad range of applications) sequencing (at the 1/8 run specification) resulted in 18.83 mega base pairs (Mbp) with an average read length of 280.06 bp. Sequence analyses of all SSR-containing clones revealed a predominance of di-nucleotide motifs (16,375, 61.5%) followed by tri-nucleotide motifs (6,616, 24.8%), tetra-nucleotide motifs (1,674, 6.3%), penta-nucleotide motifs (1,283, 4.8%), and hexa-nucleotide motifs (693, 2.6%). Among the di-nucleotide motifs, the AC/CA class was the most frequently identified (93.5% of all di-nucleotide types), followed by the GA/AG class (6.1%), the AT/TA class (0.4%), and the CG/GC class (0.03%). When we analyzed the distribution of different repeat motifs and their respective numbers of repeats, regardless of the motif class, of 100 SSR markers, we found a higher number of di-nucleotide motifs with 70 to 80 repeats; we also found two di-nucleotide motifs with 83 and 89 repeats, respectively, but their product lengths were within optimum size (297 and 300 bp). In future work, we will screen for polymorphisms of possible primer pairs. The results will provide a useful tool for assessing molecular diversity and investigating the population structure among and within Chrysanthemum species.

• Horticultural Science & Technology
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• v.32 no.6
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• pp.853-863
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• 2014

This study was carried out to construct a DNA profile database of 100 strawberry cultivars using microsatellite markers. Two hundred seventy four microsatellite primer pairs were screened with a set of 21 strawberry cultivars with different morphological traits. Twenty five primer pairs were selected because they produced reliable and reproducible fingerprints. These primer pairs were used to develop DNA profiles of 100 strawberry cultivars. Three to thirteen alleles were detected by each marker with an average of 7.50. The average polymorphism information content varied from 0.331 to 841 (average 0.706). Cluster analysis showed that the 100 cultivars were divided into 7 major groups reflecting geographic origin and pedigree information. Moreover, most of the cultivars could be discriminated by marker genotypes. These markers will be useful as a tool for the protection of plant breeders' intellectual property rights in addition to providing the means to intervene seed disputes relating to variety authentication.

• Korean Journal of Poultry Science
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• v.37 no.3
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• pp.247-253
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• 2010

Telomeres are nucleoprotein structures at the ends of chromosomes consisting of DNA sequences arranged in tandemly repeated units $(TTAGGG)_n$. However, this hexamers can also occur at non-telomeric sites in some avians and vertbrate. This study was carried out to present the distribution of telomeric DNA sequences in Korean Native Chicken chromosomes. The fluorescence in situ hybridization technique using a telomeric DNA probe was performed to the metaphase spreads of chicken early embryonic cells. Telomeric DNA signals were detected at the ends of chromosomes including macrochromosomes and microchromosomes. In chicken, surprisingly, chromosome 1 showed very distinct interstitial telomeric DNA hybridization patterns which located two interstitial sites in the p-arm at 1p11 and 1p23, and one in the q-arm at 1q32. In chromosome number 2 and 3 also displayed interstitial telomeric signals (ITS) in the long arms at 2q24 and 3q32, respectively. The pattern of telomeric DNA distribution in Korean Native Chicken chromosomes was in agreement with a previously reported in Gallus domesticus. The relative amount of telomeric DNA sequences in each macrochromosomes ranged from 4.6% to 16.3%. Distribution of telomeric DNAs at the end of p-arm was much more than that of q-arm in almost chicken chromosomes. The distribution of ITS in chicken chromsomes implicate to tandem chromosome fusions that might have occurred during the process of karyotype evolution.

• Analytical Science and Technology
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• v.31 no.2
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• pp.65-70
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• 2018

This study compared two methods for preparing ancient DNA (aDNA) for the construction of successful shotgun libraries that may be applied to massive parallel sequencing. For the comparative analysis, the DNA of prehistoric rib samples from Hungary was extracted using either a manually prepared silica suspension or the Amicon Ultracel-15 10K ultracentrifugal device (Millipore). After the extraction of the same amount of bone powder (about 150 mg) from three samples by each method, the amount of extracted double-stranded DNA and the subsequent degree of construction of the shotgun library were analyzed. The Amicon device method was rapid and easier to perform and resulted in an approximately 11-fold higher DNA recovery than that obtained using the silica suspension. The shotgun library constructed using DNA templates prepared by the Amicon device was more successful than that constructed from templates isolated using the silica suspension. The comparative study of these two aDNA extraction methods showed that the Amicon device has the advantages of saving time, process simplicity, and high efficiency.