• Genomics & Informatics
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• 제8권3호
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• pp.138-141
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• 2010

Together with single nucleotide polymorphism (SNP), copy number variations (CNV) are recognized to be the major component of human genetic diversity and used as a genetic marker in many disease association studies. Affymetrix Genome-wide SNP 5.0 is one of the commonly used SNP array platforms for SNP-GWAS as well as CNV analysis. However, there has been no report that validated the accuracy and reproducibility of CNVs identified by Affymetrix SNP array 5.0. In this study, we compared the characteristics of CNVs from the same set of genomic DNAs detected by three different array platforms; Affymetrix SNP array 5.0, Agilent 2X244K CNV array and NimbleGen 2.1M CNV array. In our analysis, Affymetrix SNP array 5.0 seems to detect CNVs in a reliable manner, which can be applied for association studies. However, for the purpose of defining CNVs in detail, Affymetrix Genome-wide SNP 5.0 might be relatively less ideal than NimbleGen 2.1M CNV array and Agilent 2X244K CNV array, which outperform Affymetrix array for defining the small-sized single copy variants. This result will help researchers to select a suitable array platform for CNV analysis.

• Genomics & Informatics
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• 제21권3호
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• pp.34.1-34.10
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• 2023

Nosocomial infections, commonly referred to as healthcare-associated infections, are illnesses that patients get while hospitalized and are typically either not yet manifest or may develop. One of the most prevalent nosocomial diseases in hospitalized patients is pneumonia, among the leading causes of mortality and morbidity. Viral, bacterial, and fungal pathogens cause pneumonia. More severe introductions commonly included Staphylococcus aureus, which is at the top of bacterial infections, per World Health Organization reports. The staphylococci, S. aureus, strain RMI-014804, mesophile, on-sporulating, and non-motile bacterium, was isolated from the sputum of a pulmonary patient in Pakistan. Many characteristics of S. aureus strain RMI-014804 have been revealed in this paper, with complete genome sequence and annotation. Our findings indicate that the genome is a single circular 2.82 Mbp long genome with 1,962 protein-coding genes, 15 rRNA, 49 tRNA, 62 pseudogenes, and a GC content of 28.76%. As a result of this genome sequencing analysis, researchers will fully understand the genetic and molecular basis of the virulence of the S. aureus bacteria, which could help prevent the spread of nosocomial infections like pneumonia. Genome analysis of this strain was necessary to identify the specific genes and molecular mechanisms that contribute to its pathogenicity, antibiotic resistance, and genetic diversity, allowing for a more in-depth investigation of its pathogenesis to develop new treatments and preventive measures against infections caused by this bacterium.

• Genomics & Informatics
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• 제21권3호
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• pp.35.1-35.12
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• 2023

The Bacillus cereus group, also known as B. cereus sensu lato (B. cereus s.l.), is composed of various Bacillus species, some of which can cause diarrheal or emetic food poisoning. Several emerging highly heat-resistant Bacillus species have been identified, these include B. thermoamylovorans, B. sporothermodurans, and B. cytotoxicus NVH 391-98. Herein, we performed whole genome analysis of two thermotolerant Bacillus sp. isolates, Bacillus sp. B48 and Bacillus sp. B140, from an omelet with acacia leaves and fried rice, respectively. Phylogenomic analysis suggested that Bacillus sp. B48 and Bacillus sp. B140 are closely related to B. cereus and B. thuringiensis, respectively. Whole genome alignment of Bacillus sp. B48, Bacillus sp. B140, mesophilic strain B. cereus ATCC14579, and thermophilic strain B. cytotoxicus NVH 391-98 using the Mauve program revealed the presence of numerous homologous regions including genes responsible for heat shock in the dnaK gene cluster. However, the presence of a DUF4253 domain-containing protein was observed only in the genome of B. cereus ATCC14579 while the intracellular protease PfpI family was present only in the chromosome of B. cytotoxicus NVH 391-98. In addition, prophage Clp protease-like proteins were found in the genomes of both Bacillus sp. B48 and Bacillus sp. B140 but not in the genome of B. cereus ATCC14579. The genomic profiles of Bacillus sp. isolates were identified by using whole genome analysis especially those relating to heat-responsive gene clusters. The findings presented in this study lay the foundations for subsequent studies to reveal further insights into the molecular mechanisms of Bacillus species in terms of heat resistance mechanisms.

• Journal of Dairy Science and Biotechnology
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• 제38권3호
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• pp.142-145
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• 2020

Enterococcus faecalis CAUM157, isolated from raw cow's milk, is a Gram-positive, facultatively anaerobic, and non-spore-forming bacterium capable of inhabiting a wide range of environmental niches. E. faecalis CAUM157 was observed to produce a two-peptide bacteriocin that had a wide range of activity against several pathogens, including Listeria monocytogenes, Staphylococcus aureus, and periodontitis-causing bacteria. The whole genome of E. faecalis CAUM157 was sequenced using the PacBio RS II platform, revealing a genome size of 2,972,812 bp with a G+C ratio of 37.44%, assembled into two contigs. Annotation analysis revealed 2,830 coding sequences, 12 rRNAs, and 61 tRNAs. Further, in silico analysis of the genome identified a single bacteriocin gene cluster.

• Journal of Microbiology and Biotechnology
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• 제22권5호
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• pp.649-653
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• 2012

A temperate phage was isolated from emetic Bacillus cereus NCTC 11143 by mitomycin C and characterized by transmission electron microscopy and DNA and protein analyses. Whole genome sequencing of Bacillus phage 11143 was performed by GS-FLX. The phage has a dsDNA genome of 39,077 bp and a 35% G+C content. Bioinformatic analysis of the phage genome revealed 49 putative ORFs involved in replication, morphogenesis, DNA packaging, lysogeny, and host lysis. Bacillus phage 11143 could be classified as a member of the Siphoviridae family by morphology and genome structure. Genomic comparisons at the DNA and protein levels revealed homologous genetic modules with patterns and morphogenesis proteins similar to those of other Bacillus phages. Thus, Bacillus phages might have a mosaic genetic relationship.

• Journal of Microbiology and Biotechnology
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• 제24권4호
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• pp.563-567
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• 2014

Pseudomonas syringae pv. syringae (Psy) is a major bacterial pathogen of many economically important plant species. Despite the severity of its impact, the genome sequence of the type strain has not been reported. Here, we present the draft genome sequence of Psy ATCC 19310. Comparative genomic analysis revealed that Psy ATCC 19310 is closely related to Psy B728a. However, only a few type III effectors, which are key virulence factors, are shared by the two strains, indicating the possibility of host-pathogen specificity and genome dynamics, even under the pathovar level.

• Genomics & Informatics
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• 제11권3호
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• pp.135-141
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• 2013

Gene set analysis is a powerful tool for interpreting a genome-wide association study result and is gaining popularity these days. Comparison of the gene sets obtained for a variety of traits measured from a single genetic epidemiology dataset may give insights into the biological mechanisms underlying these traits. Based on the previously published single nucleotide polymorphism (SNP) genotype data on 8,842 individuals enrolled in the Korea Association Resource project, we performed a series of systematic genome-wide association analyses for 49 quantitative traits of basic epidemiological, anthropometric, or blood chemistry parameters. Each analysis result was subjected to subsequent gene set analyses based on Gene Ontology (GO) terms using gene set analysis software, GSA-SNP, identifying a set of GO terms significantly associated to each trait ($p_{corr}$ < 0.05). Pairwise comparison of the traits in terms of the semantic similarity in their GO sets revealed surprising cases where phenotypically uncorrelated traits showed high similarity in terms of biological pathways. For example, the pH level was related to 7 other traits that showed low phenotypic correlations with it. A literature survey implies that these traits may be regulated partly by common pathways that involve neuronal or nerve systems.

• Journal of Microbiology and Biotechnology
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• 제29권5호
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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.

• Journal of Microbiology and Biotechnology
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• 제31권4호
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• pp.601-609
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• 2021

Erythrobacter species are extensively studied marine bacteria that produce various carotenoids. Due to their photoheterotrophic ability, it has been suggested that they play a crucial role in marine ecosystems. It is essential to identify the genome sequence and the genes of the species to predict their role in the marine ecosystem. In this study, we report the complete genome sequence of the marine bacterium Erythrobacter sp. 3-20A1M. The genome size was 3.1 Mbp and its GC content was 64.8%. In total, 2998 genetic features were annotated, of which 2882 were annotated as functional coding genes. Using the genetic information of Erythrobacter sp. 3-20A1M, we performed pan-genome analysis with other Erythrobacter species. This revealed highly conserved secondary metabolite biosynthesis-related COG functions across Erythrobacter species. Through subsequent secondary metabolite biosynthetic gene cluster prediction and KEGG analysis, the carotenoid biosynthetic pathway was proven conserved in all Erythrobacter species, except for the spheroidene and spirilloxanthin pathways, which are only found in photosynthetic Erythrobacter species. The presence of virulence genes, especially the plant-algae cell wall degrading genes, revealed that Erythrobacter sp. 3-20A1M is a potential marine plant-algae scavenger.

• 한국생명과학회:학술대회논문집
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• 한국생명과학회 2003년도 제40회 국제학술심포지움
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• pp.14-27
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• 2003

The genomes of Arabidopsis and rice have been fully sequenced. Genomic sequencing provides global information about genome structure and organization. A comprehensive research account of our recent studies conducted on genome painting, comparative genomics and genome fusion is provided in order to project the prospects of plant cytogenetic research in post-genomics era. Genome analysis by GISH using genome painting is demonstrated as an excellent means suitable for visualization of a whole genome, since total genomic DNA representing the overall molecular composition of the genome is used as a probe. FISH on extended DNA fibers has been developed for high-resolution FISH and has contributed to determining the copy number and order of genes. We have also mapped a number of genes involving starch synthesis on wheat chromosomes by FISH and compared the position of these genes on linkage map of rice. Macro synteny between wheat and rice can be observed by comparing the location of these genes in spite of the fact that the size of DNA per chromosome differs by 20 fold in two. Moreover, to approach our goal towards making bread and udon noodles from rice flour in future by incorporating bread making and the noodle qualifies in rice, we have been successful in introducing large genomic DNA fragments containing agronomically important genes of wheat into a rice by successive introduction of large insert BAC clones, there by expanding genetic variability in rice. We call this method genome fusion.