• KIISE Transactions on Computing Practices
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• v.20 no.9
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• pp.513-518
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• 2014

It has become possible for small scale laboratories to interpret large scale genomic DNA, thanks to the reduction of the sequencing cost by the development of next generation sequencing (NGS). De novo assembly is a method which creates a putative original sequence by reconstructing reads without using a reference sequence. There have been various study results on de novo assembly, however, it is still difficult to get the desired results even by using the same assembly procedures and the analysis tools which were suggested in the studies reported. This is mainly because there are no specific guidelines for the assembly procedures or know-hows for the use of such analysis tools. In this study, to resolve these problems, we introduce steps to finding whole genome of an unknown DNA via NGS technology and de novo assembly, while providing the pros and cons of the various analysis tools used in each step. We used 350Mbp of Toxocara canis DNA as an application case for the detailed explanations of each stated step. We also extend our works for prediction of protein-coding genes and their functions from the draft genome sequence by comparing its homology with reference sequences of other nematodes.

• Korean Journal of Ichthyology
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• v.32 no.2
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• pp.39-48
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• 2020

The slender shinner (Pseudopungtungia tenuicorpa), a tiny freshwater fish of about 8 to 10 cm belonging to Cyprinidae, is an endangered species found only in the Han and Imjin Rivers on the Korean Peninsula. During the breeding season, this species spawns in nests of Coreoperca herzi, a predator of this species, or small crevices on rocks. This unique reproductive ecology can make this species more vulnerable to anthropogenic perturbance that can further limit the places to spawn. Here, mtDNA and microsatellite loci were analyzed to identify the genetic diversity and structure of slender shinners and further to provide the basic data necessary for the conservation planning of this species. A total of 28 polymorphic microsatellite markers were developed using Illumina paired-end sequencing, and 67 slender shinners collected from three localities in the Han River were genotyped using these loci. This species showed a remarkably high level of genetic diversity with mean expected heterozygosity of 0.914 and mean allele number per locus of 27.9, and no signature of drastic demographic decline was detected. As a result of our microsatellite analysis, the genetic structure between the two stems of the Han River, North Han and South Han, was prominent. Such a genetic structure was also evident in the sequence analysis of 14 haplotypes obtained from mtDNA control region. Although slender shinners are only found in very limited areas around the world, the genetic structure indicates that there is a block of gene flow among the populations, which should be reviewed in the future if management and restoration of this species is needed.

• Journal of the Korean Institute of Telematics and Electronics S
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• v.35S no.9
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• pp.53-62
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• 1998

In this paper, a genetic algorithm-based optimization technique for stereo matching is proposed. Stereo matching is an essential process to recover three-dimensional structure of objects. The proposed two-dimensional chromosomes consist fo disparity values. The cost function of each chromosome is composed of the intensity-difference between two images and smoothness of disparity. The crossover and mutation operators in the two-dimensional chromosomes are described. The operations are affected by the disparities of neighbor pixels. The knowledge-augmented operators are shown to result in rapid convergence and stable result. The genetic algorithm for stereo matching is tested on synthetic and natural images. Experimental results of various images show that the proposed algorithm has good performance even if the images have too dense or sparse feature points. severe noise, and repeating pattern.

• Korean Journal of Poultry Science
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• v.41 no.4
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• pp.305-311
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• 2014

Copy number variation (CNV) is a form of structural variation that shows various numbers of copies in segments of the DNA. It has been shown to account for phenotypic variations in human diseases and agricultural production traits. Currently, most of chicken breeds in the poultry industry are based on European-origin breeds that have been mostly provided from several international breeding companies. Therefore, National Institute of Animal Science, RDA has been trying to restore and improve Korean native chicken breeds (12 lines of 5 breeds) for about 20 years. Thanks to the recent advance of sequencing technologies, genome-wide CNV can be accessed in the higher resolution throughout the genome of species of interest. However, there is no systematic study available to dissect the CNV in the native chicken breed in Korea. Here, we report genome-wide copy number variations identified from a genome of Korean native chicken (Line L) by comparing between the chicken reference sequence assembly (Gallus gallus) and a de novo sequencing assembly of the Korean native chicken (Line L). Throughout all twenty eight chicken autosomes, we identified a total of 501 CNVs; defined as gain and loss of duplication and deletion respectively. Furthermore, we performed gene ontology (GO) analysis for the putative CNVs using DAVID, leading to 68 GO terms clustered independently. Of the clustered GO terms, genes related to transcription and gene regulation were mainly detected. This study provides useful genomic resource to investigate potential biological implications of CNVs with traits of interest in the Korean native chicken.

• Korean Journal of Microbiology
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• v.44 no.2
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• pp.93-97
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• 2008

RraA is a recently discovered protein inhibitor that regulates the enzymatic activity of RNase E, which plays a major role in the decay and processing of RNAs in Escherichia coli. It has also been shown to regulate the activity of RNase ES, a functional Streptomyces coelicolor ortholog of RNase E, which has 36% identity to the amino-terminal region of RNase E. There are two open reading frames in S. coelicolor genome that can potentially encode proteins having more than 35.4% similarity to the amino acid sequence of RraA. DNA fragment encoding one of these RraA orthologs, designated as RraAS2 here, was amplified and cloned in to E. coli vector to test whether it has ability to regulate RNase E activity in E. coli cells. Co-expression of RraAS2 partially rescued E. coli cells over-producing RNase E from growth arrest, although not as efficiently as RraA, induced by the increased ribonucleolytic activity in the cells. The copy number of ColEl-type plasmid in these cells was also decreased by 14% compared to that in cells over-producing RNase E only, indicating the ability of RraAS2 to inhibit RNase E action on RNA I. We observed that the expression level of RraAS2 was lower than that of RraA by 4.2 folds under the same culture condition, suggesting that because of inefficient expression of RraAS2 in E. coli cells, co-expression of RraAS2 was not efficiently able to inhibit RNase E activity to the level for proper processing and decay of all RNA species that is required to restore normal cellular growth to the cells over-producing RNase E.

• Journal of Plant Biotechnology
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• v.44 no.2
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• pp.171-177
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• 2017

A callus-mediated regeneration protocol for sea-milkwort, an endangered coastal plant species in South Korea, is reported here. The explants of in vitro-plantlets generated from a node culture revealed distinguishable responses in callus induction depending on genotype, explant source, light condition, and 2,4-D concentration. Especially, continuous darkness exclusively facilitated callus induction from explants prior to other treatments. The calli initiated on the media with 2,4-D ranging from 0.1 mg/L to 3.0 mg/L in the dark vigorously proliferated when subcultured on the same media in continuous darkness. Given 1.0 mg/L zeatin in addition to darkness to the calli of the 'Pistachio' genotype, normal adventitious shoots were only regenerated from nodular structures that formed earlier from the calli at the frequency of 24.4 percent. Regenerated shoots easily grew into plantlets with roots and green color on a phytohormone-free MS medium under lighted condition, that were used for node culture as plant materials. Node culture effectively multiplied plantlets in accordance with protocol by Bae et al. (2016). Acclimatized plantlet clusters developed mature plant clusters under inland environment, followed by flowering the following April. Results were merged with node culture protocol suggested by Bae et al. (2016), which, as an in vitro propagation system for sea-milkwort, may contribute to natural habitat restoration.

• Journal of Aquaculture
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• v.19 no.4
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• pp.281-287
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• 2006

Intraspecific diploid androgenesis was achieved in mud loach (Misgurnus mizolepis) by the inhibition of the first mitotic division using combined thermal treatment. A combined thermal treatment (heat shock at $40.5\;^{\circ}C$ for 120 sec followed by cold treatment at $1\;^{\circ}C$ for 45 min) applied to the 1st metaphase of cell division (28 min post insemination at $25\;^{\circ}C$) successfully recovered viable androgenetic diploidy. Mean hatching success of the androgenetic diploid group was 29.6%, and the average yield out of total eggs taken was about 7% assessed at 1 week of age. However, relatively large variations in the yield of diploid androgenesis were observed among different egg batches used as cytoplasmic donors. Successful diploidization was confirmed by flow cytometric analysis, and parthenogenic reproduction in a paternal exclusive manner was verified with transgene dosage. Significant mortality was found in most androgenetic groups especially from hatch to 1 month of age, although such mortality was stabilized later.