• Proceedings of the Korean Society of Plant Pathology Conference
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• 2003.10a
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• pp.115.2-116
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• 2003

Complete genomic nucleotide sequence of Daphe virus S (DVS), a member of the genus Carlavirus, causing leaf distortion and chlorotic spot disease symptoms in daphne plants, has been determined in this study. The genome of DVS contained six open reading fames coding for long viral replicase, triple gene block, 36 kDa viral coat protein (CP) and 12 kDa from the 5' to 3' ends, which is a typical genome structure of carlaviruses. Two Korean isolates of DVS isolates were 98.1％ and 93.6％ amino acid identical in the CP and 12kDa, respectively. The CP gene of DVS shares 25.2-55.2％ and 42.9-56.1％ similarities with that of 19 other carlaviruses at the amino acid and nucleotide levels, respectively. The 3'-proximal 12 kDa gene of DVS shares 20.2-57.8％ amino acid identities with that of 18 other members of the genus. The 3' noncoding region of DVS consists of 73 nucleotides with long excluding poly A tract, and shares 69.1-77.1％ identities to the known carlaviruses. In the phylogenetic analyses of the two proteins, DVS was closely related to Helenium virus S and Chrysanthemum virus B. This is the first complete sequence information for the DVS, and further confirms the classification of DVS as a distinct species of the genus Carlavirus.

• BMB Reports
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• v.37 no.1
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• pp.75-82
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• 2004

Recent years saw a dramatic increase in genomic and proteomic data in public archives. Now with the complete genome sequences of human and other species in hand, detailed analyses of the genome sequences will undoubtedly improve our understanding of biological systems and at the same time require sophisticated bioinformatic tools. Here we review what computational challenges are ahead and what are the new exciting developments in this exciting field.

• Genomics & Informatics
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• v.2 no.4
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• pp.184-190
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• 2004

An approach for genome analysis based on assembly of fragments of DNA from the whole genome can be applied to obtain the complete nucleotide sequence of the genome of Zymomonas mobilis. However, the problem of fragment assembly raise thorny computational issues. Computer simulation studies of sequence assembly usually show some abnormal assemblage of artificial sequences containing repetitive or duplicated regions, and suggest methods to correct those abnormalities. In this paper, we describe five simulation studies which had been performed previous to the actual genome assembly process of Zymomonas mobilis ZM4.

• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.237-237
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• 2022

Cynodon transvaalensis belongs to the warm-season grasses and is one of the economically and ecologically important crops. Cynodon species with high heterozygosity are difficult to assemble, so genome research has not been actively conducted. In this study, hybrid assembly was performed by sequencing with Illumina and PacBio. As a result of the assembly, the number of scaffolds and the length of N50 were 1,392, 928 kb, respectively. The completeness of the assembly was confirmed by BSUCO at 98.3%. In addition, as a result of estimating the size of the assembled genome by K-mer analysis (k=25), it was approximately ~413 Mb. A total of 37,060 cds sequences were annotated in the assembled genome, and their functions were identified through blast. After that, we try to complete the assembled genome into a pseudochromosome-level genome through Hi-C technology. These results will not only help to understand the complex genome composition of african bermudagrass, but also provide a resource for genomic and evolutionary studies of grass and other plant species.

• Proceedings of the Korean Society of Applied Entomolohy Conference
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• 2002.05a
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• pp.178-178
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• 2002

• Proceedings of the Korean Society of Sericultural Science Conference
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• 2002.04a
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• pp.69-69
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• 2002

No Abstract, See Full Text

• Journal of Microbiology and Biotechnology
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• v.29 no.5
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• pp.794-808
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• 2019

Bacillus velezensis strain WRN014 was isolated from banana fields in Hainan, China. Bacillus velezensis is an important member of the plant growth-promoting rhizobacteria (PGPR) which can enhance plant growth and control soil-borne disease. The complete genome of Bacillus velezensis WRN014 was sequenced by combining Illumina Hiseq 2500 system and Pacific Biosciences SMRT high-throughput sequencing technologies. Then, the genome of Bacillus velezensis WRN014, together with 45 other completed genome sequences of the Bacillus velezensis strains, were comparatively studied. The genome of Bacillus velezensis WRN014 was 4,063,541bp in length and contained 4,062 coding sequences, 9 genomic islands and 13 gene clusters. The results of comparative genomic analysis provide evidence that (i) The 46 Bacillus velezensis strains formed 2 obviously closely related clades in phylogenetic trees. (ii) The pangenome in this study is open and is increasing with the addition of new sequenced genomes. (iii) Analysis of single nucleotide polymorphisms (SNPs) revealed local diversification of the 46 Bacillus velezensis genomes. Surprisingly, SNPs were not evenly distributed throughout the whole genome. (iv) Analysis of gene clusters revealed that rich gene clusters spread over Bacillus velezensis strains and some gene clusters are conserved in different strains. This study reveals that the strain WRN014 and other Bacillus velezensis strains have potential to be used as PGPR and biopesticide.

• The Korea Genome Conference
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• 2004.07a
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• pp.41.1-41.1
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• 2004

• Proceedings of the Korean Society of Sericultural Science Conference
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• 2002.10a
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• pp.137-137
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• 2002

No Abstract, See Full Text

• Korean Journal of Microbiology
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• v.52 no.4
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• pp.500-502
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• 2016

Several bacterial species have been reported to be surviving after the ionizing radiation treatment due to the presence of sophisticated enzymes systems and some endospores producing bacterial strains can also resist, due to the presence of thick spore coat. In this study, we report the complete genome sequence of a bacterium Paenibacillus swuensis $DY6^T$, isolated from an irradiated soil sample. The genome comprised of 5,012,599 bp with the G+C content of 49.93%, the genome included 4,463 protein coding genes and 133 RNA genes.