• Journal of Microbiology and Biotechnology
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• v.25 no.1
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• pp.98-108
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• 2015

Staphylococcus aureus is an important foodborne pathogen that causes diverse diseases ranging from minor infections to life-threatening conditions in humans and animals. To further understand its pathogenesis, the genome of the strain S. aureus FORC_001 was isolated from a contaminated food. Its genome consists of 2,886,017 bp double-stranded DNA with a GC content of 32.8%. It is predicted to contain 2,728 open reading frames, 57 tRNAs, and 6 rRNA operons, including 1 additional 5S rRNA gene. Comparative phylogenetic tree analysis of 40 complete S. aureus genome sequences using average nucleotide identity (ANI) revealed that strain FORC_001 belonged to Group I. The closest phylogenetic match was S. aureus MRSA252, according to a whole-genome ANI (99.87%), suggesting that they might share a common ancestor. Comparative genome analysis of FORC_001 and MRSA252 revealed two non-homologous regions: Regions I and II. The presence of various antibiotic resistance genes, including the SCCmec cluster in Region I of MRSA252, suggests that this strain might have acquired the SCCmec cluster to adapt to specific environments containing methicillin. Region II of both genomes contains prophage regions but their DNA sequence identity is very low, suggesting that the prophages might differ. This is the first report of the complete genome sequence of S. aureus isolated from a real foodborne outbreak in South Korea. This report would be helpful to extend our understanding about the genome, general characteristics, and virulence factors of S. aureus for further studies of pathogenesis, rapid detection, and epidemiological investigation in foodborne outbreak.

• Korean Journal of Plant Taxonomy
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• v.50 no.1
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• pp.8-16
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• 2020

Complete chloroplast genome sequences provide detailed information about any structural changes of the genome, instances of phylogenetic reconstruction, and molecular markers for fine-scale analyses. Recent developments of next-generation sequencing (NGS) tools have led to the rapid accumulation of genomic data, especially data pertaining to chloroplasts. Short reads deposited in public databases such as the Sequence Read Archive of the NCBI are open resources, and the corresponding chloroplast genomes are yet to be completed. The V. dilatatum complex in Korea consists of four morphologically similar species: V. dilatatum, V. erosum, V. japonicum, and V. wrightii. Previous molecular phylogenetic analyses based on several DNA regions did not resolve the relationship at the species level. In order to examine the level of variation of the chloroplast genome in the V. dilatatum complex, raw reads of V. dilatatum deposited in the NCBI database were used to reconstruct the whole chloroplast genome, with these results compared to the genomes of V. erosum, V. japonicum, and three other species in Viburnum. These comparative genomics results found no significant structural changes in Viburnum. The degree of interspecific variation among the species in the V. dilatatum complex is very low, suggesting that the species of the complex may have been differentiated recently. The species of the V. dilatatum complex share large unique deletions, providing evidence of close relationships among the species. A phylogenetic analysis of the entire genome of the Viburnum showed that V. dilatatum is a sister to one of two accessions of V. erosum, making V. erosum paraphyletic. Given that the overall degree of variation among the species in the V. dilatatum complex is low, the chloroplast genome may not provide a phylogenetic signal pertaining to relationships among the species.

• Korean journal of applied entomology
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• v.61 no.3
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• pp.507-512
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• 2022

The Gypsy moth, Lymantria dispar (Linnaeus, 1758) (Lepidoptera: Erebidae) is a serious pest that attacks forest as well as fruit trees. We sequenced the 15,548 bp long complete mitochondrial genome (mitogenome) of this species. It consists of a typical set of genes (13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes) and one major non-coding A + T-rich region. The orientation and gene order of the L. dispar mitogenome are identical to that of the ancestral type found in majority of the insects. Phylogenetic analyses using concatenated sequences of 13 PCGs and 2 rRNAs (13,568 bp including gaps) revealed that the L. dispar examined in our study, together with other geographical samples of L. dispar in a group forming the family Erebidae and consistently supported the monophyly of each family (Erebidae, Euteliidae, Noctuidae, Nolidae and Notodontidae), generally with the highest nodal supports.

• Animal Systematics, Evolution and Diversity
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• v.28 no.1
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• pp.36-41
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• 2012

The larvae of Chaoborus are widely distributed in lakes, ponds, and reservoirs. These omnivorous Chaoborus larvae are crucial predators and play a role in structuring zooplankton communities, especially for small-sized prey. Larvae of Chaoborus are commonly known to produce predator-induced polyphenism in Daphnia sp. Nevertheless, their taxonomy and molecular phylogeny are very poorly understood. As a fundamental study for understanding the role of Chaoborus in predator-prey interactions in a freshwater ecosystem, the molecular identification and phylogenetic relationship of Chaoborus were analyzed in this study. A molecular comparison based on partial mitochondrial cytochrome oxidase I (COI) between species in Chaoborus was carried out for the identification of Chaoborus larvae collected from 2 localities in Korea. According to the results, the Chaoborus species examined here was identified as C. flavicans, which is a lake-dwelling species. Furthermore, partial mitochondrial genome including COI, COII, ATP6, ATP8, COIII, and ND3 were also newly sequenced from the species and concatenated 5 gene sequences excluding ATP8 with another 9 dipteran species were compared to examine phylogenetic relationships of C. flavicans. The results suggested that Chaoborus was more related to the Ceratopogonidae than to the Culicidae. Further analysis based on complete mitochondrial DNA sequences and nuclear gene sequences will provide a more robust validation of the phylogenetic relationships of Chaoborus within dipteran lineages.

• Research in Plant Disease
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• v.19 no.2
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• pp.77-83
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• 2013

Bean yellow mosaic virus (BYMV; genus Potyvirus, family Potyviridae) causes severe losses to various legume species and a number of non-legume species, particularly freesia plants. In a survey of virus diseases in Gyeonggi province, Korea, BYMV isolates were identified from many cultivated freesia species. Here, we determined the complete nucleotide sequences of a BYMV freesia isolate (BYMV-Fr; accession number FJ492961). BYMV-Fr genome consists of 9,545 nucleotides (nt) excluding the poly (A) tail and encodes 3,057 amino acid (aa), with an AUG start and UAG stop codon, containing one open reading frame typical of a potyvirus polyprotein. The polyprotein of BYMV-Fr was divided to ten proteins and the cleavage sites of each protein were determined. The coat protein (CP) and polyprotein of BYMV-Fr were compared at the aa level with those of the previously reported 4 BYMV isolates. BYMV-Fr shared 90.1 to 97.1 and 91.0 to 92.5% at the CP and polyprotein homology. Interestingly, BYMV-Fr showed identities of a lower level at the nt level of 5' noncoding region (61.4 to 67.6%) and at the aa level of P1 (71.4 to 72.8%), comparing with four BYMV isolates. Based on the aa sequence diversity of CP and polyprotein, phylogenetic analysis with the four BYMV isolates showed two distinct groups and BYMV-Fr and most BYMV isolates were most closely related to the clover yellow vein virus among 52 potyviruses. To our knowledge, this is the first report of the complete genome sequence of BYMV freesia strain.

• Korean Journal of Microbiology
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• v.54 no.3
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• pp.283-285
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• 2018

Azoarcus are known to contain bacterial strains usually found in contaminated areas. Two strains of Azoarcus sp., TSPY31 and TSNA42, were isolated from oil-contaminated marine tidal flats, and their genomic structures were analyzed. The genomes of both TSPY31 and TSNA42 were composed of a single complete chromosome of 4,572,082 bp (G + C content: 63.2%) and 4,886,934 bp (G + C content: 62.8%), respectively. Both genomes were found to contain two copies of styrene monooxygenases that are predicted to be responsible for converting indole to indigo.

• Journal of Applied Biological Chemistry
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• v.63 no.3
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• pp.189-195
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• 2020

The soybean (Glycine max L.), also known as the soya bean, is an economically important legume species. Pathogens are always major threats for soybean cultivation. Several pathogens negatively affect soybean production. The soybean is also known as a susceptible host to many viruses. Recently, we carried out systematic analyses to identify viruses infecting soybeans using soybean transcriptome data. Our screening results showed that only few soybean transcriptomes contained virus-associated sequences. In this study, we further carried out bioinformatics analyses using a soybean flower bud transcriptome for virus identification, genome assembly, and single nucleotide variations (SNVs). We assembled the genome of Soybean yellow common mosaic virus (SYCMV) isolate China and revealed two SNVs. Phylogenetic analyses using three viral proteins suggested that SYCMV isolate China is closely related to SYCMV isolates from South Korea. Furthermore, we found that replication and mutation of SYCMV is relatively low, which might be associated with flower bud tissue. The most interesting finding was that SYCMV was not detected in the cytoplasmic male sterility (CMS) line derived from the non-CMS line that was severely infected by SYCMV. In summary, in silico analyses identified SYCMV from the soybean flower bud transcriptome, and a nearly complete genome of SYCMV was successfully assembled. Our results suggest that the low level of virus replication and mutation for SYCMV might be associated with plant tissues. Moreover, we provide the first evidence that male sterility might be used to eliminate viruses in crop plants.

• Korean Journal of Microbiology
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• v.55 no.1
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• pp.69-73
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• 2019

During screening of microbes for compounds having cosmetic benefits, we isolated Marinobacter salarius HL2708#2 from lava seawater on Jeju Island, Republic of Korea. The complete genome sequence was determined. Strain HL27080#2 features a circular chromosome of 4,304,603 bp with 57.21% G+C content and a 244,163 bp plasmid with 53.14% G+C. There were 4,180 protein coding sequences identified, along with 49 transfer RNA and 18 ribosomal RNA noncoding genes. The genome harbored genes for the utilization of alcohol, maltose/starch, and monosaccharide as sole carbon sources. Genes responsible for halophilic characteristics and heavy metal resistance could be annotated, as well as aromatic and alkane hydrocarbons. Contrary to the prior report that M. salarius is negative for nitrate and nitrite reduction, nitrate/nitrite reductase along with nitrate/nitrate transporters and nitronate monooxygenase were evident, suggesting that strain HL2708#2 may be able to denitrify extracellular nitroalkenes to ammonia.

• Journal of Animal Science and Technology
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• v.46 no.6
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• pp.937-946
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• 2004

Duroc is widely used to improve the meat quality and productivity. To elucidate the phylogenetic relation and the sequence specificity for the maternal property, the complete sequence of mitochondrial genome was determined and the population diversity of Duroc was investigated in this study. The length of mtDNA tested is 16,584-bp. There are several insertion/deletion mutations in the control region and coding regions for tRNA and rRNA, respectively, but not in peptide-coding regions. Four peptide-coding genes(COⅡ, COⅢ, ND3 and ND4) showed incomplete termination codon sequences such as T--, and two(ND2 and ND4L) did alternative initiation codons(AIC), respectively. Especially, the initiation codon sequences of ND2 gene were polymorphic in this population. Polymorphisms were detected in 11-bp duplication motif within control region as well as ND2 and CYTB. Variation patterns observed from the tests on three mtDNA regions were linked completely and then two haplotypes obtained from combining the data dividing this population. Duroc mtDNA is observed at the European pig cluster in the phylogenetic tree, however, the results from the population analyses supported previous opinions. This study suggests that the breed Duroc was mainly originated from the European pig lineage, and Asian lineage was also used to form the pig breed Duroc as maternal progenitors.

• Asian-Australasian Journal of Animal Sciences
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• v.14 no.6
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• pp.880-884
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• 2001

Rumen microbiology research has undergone several evolutionary steps: the isolation and nutritional characterization of readily cultivated microbes; followed by the cloning and sequence analysis of individual genes relevant to key digestive processes; through to the use of small subunit ribosomal RNA (SSU rRNA) sequences for a cultivation-independent examination of microbial diversity. Our knowledge of rumen microbiology has expanded as a result, but the translation of this information into productive alterations of ruminal function has been rather limited. For instance, the cloning and characterization of cellulase genes in Escherichia coli has yielded some valuable information about this complex enzyme system in ruminal bacteria. SSU rRNA analyses have also confirmed that a considerable amount of the microbial diversity in the rumen is not represented in existing culture collections. However, we still have little idea of whether the key, and potentially rate-limiting, gene products and (or) microbial interactions have been identified. Technologies allowing high throughput nucleotide and protein sequence analysis have led to the emergence of two new fields of investigation, genomics and proteomics. Both disciplines can be further subdivided into functional and comparative lines of investigation. The massive accumulation of microbial DNA and protein sequence data, including complete genome sequences, is revolutionizing the way we examine microbial physiology and diversity. We describe here some examples of our use of genomics- and proteomics-based methods, to analyze the cellulase system of Ruminococcus flavefaciens FD-1 and explore the genome of Ruminococcus albus 8. At Illinois, we are using bacterial artificial chromosome (BAC) vectors to create libraries containing large (>75 kbases), contiguous segments of DNA from R. flavefaciens FD-1. Considering that every bacterium is not a candidate for whole genome sequencing, BAC libraries offer an attractive, alternative method to perform physical and functional analyses of a bacterium's genome. Our first plan is to use these BAC clones to determine whether or not cellulases and accessory genes in R. flavefaciens exist in clusters of orthologous genes (COGs). Proteomics is also being used to complement the BAC library/DNA sequencing approach. Proteins differentially expressed in response to carbon source are being identified by 2-D SDS-PAGE, followed by in-gel-digests and peptide mass mapping by MALDI-TOF Mass Spectrometry, as well as peptide sequencing by Edman degradation. At Ohio State, we have used a combination of functional proteomics, mutational analysis and differential display RT-PCR to obtain evidence suggesting that in addition to a cellulosome-like mechanism, R. albus 8 possesses other mechanisms for adhesion to plant surfaces. Genome walking on either side of these differentially expressed transcripts has also resulted in two interesting observations: i) a relatively large number of genes with no matches in the current databases and; ii) the identification of genes with a high level of sequence identity to those identified, until now, in the archaebacteria. Genomics and proteomics will also accelerate our understanding of microbial interactions, and allow a greater degree of in situ analyses in the future. The challenge is to utilize genomics and proteomics to improve our fundamental understanding of microbial physiology, diversity and ecology, and overcome constraints to ruminal function.