• 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.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2018.04a
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• pp.40-40
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• 2018

Pseudostellaria Pax (Caryophyllaceae) is a small genus distributed in temperate region. It consists of 25 species presenting high diversity in Asia. Pseudostellaria longipedicellata S. Lee, K. Heo & S. C. Kim was first announced as new species in 2012. Morphological characters of P. longipedicellata are closely related to those of Psedusotellaria palibiniana and Psedusotellaria okmotoi. These are distinguished from P. longipedicellata by shorter pedicel and puberulent pedicels, respectively and by being distributed allopatically between P. longipedicellata and rest of species. The complete chloroplast genome of P. longipedicellata was successfully rescued from raw reads generated by HiSeq2000. Its total length is 149,626 bp consisting of four regions: large single copy (LSC) region (81,292 bp), small single copy (SSC) region (16,984bp), and inverted repeats (IRs; 25,765 bp per each). It contained 126 genes (81 coding DNA sequence (CDS), eight rRNAs, and 37 tRNAs); 18 genes (seven CDS, four rRNAs, and seven tRNAs) are duplicated in inverted repeat regions. The overall GC content of P. longipedicellata is 36.5% and in the LSC, SSC, and IR regions were 34.3%, 29.3%, and 42.4%, respectively. Based on phylogenetic analysis of chloroplast genomes of P. longipedicellata and relatives species presents clear phylogenetic positions of Pseudostellaria genus. This chloroplast genome will be an important sequence resources for further researches of Pseudostellaria genus.

• Korean Journal of Microbiology
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• v.54 no.3
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• pp.305-307
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• 2018

The whole genome sequencing using PacBio RS II platform was performed for a marine bacterium Pseudoalteromonas donghaensis $HJ51^T$ isolated from East Sea of Korea. As a result, three assembled contigs consisting of a chromosome (size of 3,646,857 bp, and G + C content of 41.8%) and two plasmids (size of 842,855 bp and 244,204 bp, and G + C content of 41.3% and 40.4%, respectively) were obtained. The genome included 4,083 protein coding genes and 127 RNA genes. This result could be used for gene sources of biopolymers degradation and the development as a new host with secretion system similar to Escherichia coli.