• International Journal of Industrial Entomology and Biomaterials
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• v.46 no.2
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• pp.41-54
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• 2023

The blue-tailed damselfly, Ischnura elegans Van der Linden, 1820 (Odonata: Coenagrionidae), is a climate-sensitive indicator species in South Korea. In this study, we sequenced the complete mitochondrial genome (mitogenome) of I. elegans collected from South Korea for subsequent population genetic analysis, particularly to trace population movements in response to climate change. The 15,963 base pair (bp)-long complete mitogenome of I. elegans has typical sets of genes including a major non-coding region (the A+T-rich region), and an arrangement identical to that observed in ancestral insect species. The ATP6, ND3 and ND1 genes have the TTG start codon, which, although rare, is the canonical start codon for animal mitochondrial tRNA. The A/T content was 71.4% in protein-coding genes, 72.1% in tRNAs, 72.9% in the whole genome, 74.7% in srRNA, 75.3% in lrRNA, and 83.8% in the A+T-rich region. The A+T-rich region is unusually long (1,196 bp) and contains two subunits (192 bp and 176-165 bp), each of which is tandemly triplicated and surrounded by non-repeat sequences. Comparison of the sequence divergence among available mitogenomes of I. elegans, including the one from the current study, revealed ND2 as the most variable gene, followed by COII and COI, suggesting that ND2 should be targeted first in subsequent population-level studies. Phylogenetic reconstruction based on all available mitogenome sequences of Coenagrionidae showed a strong sister relationship between I. elegans and I. senegalensis.

• Journal of Microbiology and Biotechnology
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• v.33 no.6
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• pp.753-759
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• 2023

The genus Paenibacillus contains a variety of biologically active compounds that have potential applications in a range of fields, including medicine, agriculture, and livestock, playing an important role in the health and economy of society. Our study focused on the bacterium SS4^T (KCTC 43402^T = GDMCC 1.3498^T), which was characterized using a polyphasic taxonomic approach. This strain was analyzed using antiSMASH, BAGEL4, and PRISM to predict the secondary metabolites. Lassopeptide clusters were found using all three analysis methods, with the possibility of secretion. Additionally, PRISM found three biosynthetic gene clusters (BGC) and predicted the structure of the product. Genome analysis indicated that glucoamylase is present in SS4^T. 16S rRNA sequence analysis showed that strain SS4^T most closely resembled Paenibacillus marchantiophytorum DSM 29850^T (98.22%), Paenibacillus nebraskensis JJ-59^T (98.19%), and Paenibacillus aceris KCTC 13870^T (98.08%). Analysis of the 16S rRNA gene sequences and Type Strain Genome Server (TYGS) analysis revealed that SS4^T belongs to the genus Paenibacillus based on the results of the phylogenetic analysis. As a result of the matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF/MS) results, SS4^T was determined to belong to the genus Paenibacillus. Comparing P. marchantiophytorum DSM 29850^T with average nucleotide identity (ANI 78.97%) and digital DNA-DNA hybridization (dDDH 23%) revealed values that were all less than the threshold for bacterial species differentiation. The results of this study suggest that strain SS4^T can be classified as a Paenibacillus andongensis species and is a novel member of the genus Paenibacillus.

• The Journal of Natural Sciences
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• v.18 no.1
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• pp.47-53
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• 2007

In order to find novel sRNA in Bacillus subtilis which would be used to adapt to several conditions, we searched the whole genome of Bacillus subtilis using the following procedure. At first, the locations of recognition sequence of transcription factors such as PerR, OhrR, Fur and Zur were searched in the intergenic region of Bacillus subtilis genome and the locations of rho independent transcription terminator sites were also determined. Based on the information of these locations, the sRNA candidates were chosen by close locations (less than 300 bp) between the recognition site of transcription factors and rho independent transcription terminator site. Than transcription promoter sites were searched in the region of previously identified sRNA candidates and 5 PerR, 1 OhrR, 1 Fur and 1 Zur regulated good sRNA candidates were found.

• Proceedings of the Korean Information Science Society Conference
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• 2008.06c
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• pp.217-221
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• 2008

생명공학 기술의 발달로 지놈 프로젝트를 통해 인간 초파리 등 여러 종의 유전체 정보가 밝혀 졌다. 그러나 Post-Genome 연구에 있어서 매우 중요한 생물체인 멍게(Ciona intestinalis)와 성게(Strongylocentrotus purpuratus)의 유전체 서열은 현재 공개되어 있으나 염기서열의 연속성(continuity)에는 심각한 문제점이 존재하고 있다. 이들은 염기서열에 변이가 많은 다염기변이 유전체(polymorphic genomes)로 그 특성이 반영되지 않은 전통적인 Whole Genome Shotgun Sequencing(WGSS)방법을 사용였기 때문이다. 이와 같은 다염기변이 유전체 서열 분석은 시스템 생물학이나 비교 유전체학 등의 후발 연구에 기초가 되므로 매우 중요하다. 본 논문에서는 다염기변이 유전체에 대해 알아보고 서열 조립 알고리즘의 기본이 되는 서열 정렬 툴들 중 가장 많이 사용되는 FASTA, BLAST, BLAT에 대해 분석하여 봄으로써 다염기변이 유전체에 적합한 서열 조립 전략 수립을 위해 고려해야 하는 사항들을 논의해 본다.

• Genomics & Informatics
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• v.20 no.2
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• pp.24.1-24.8
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• 2022

Hypomyelinating leukodystrophy type 2 (HLD2), is an inherited genetic disease of the central nervous system caused by recessive mutations in the gap junction protein gamma 2 (GJC2/GJA12). HLD2 is characterized by nystagmus, developmental delay, motor impairments, ataxia, severe speech problem, and hypomyelination in the brain. The GJC2 sequence encodes connexin 47 protein (Cx47). Connexins are a group of membrane proteins that oligomerize to construct gap junctions protein. In the present study, a novel missense mutation gene c.760G>A (p.Val254Met) was identified in a patient with HLD2 by performing whole exome sequencing. Following the discovery of the new mutation in the proband, we used Sanger sequencing to analyze his affected sibling and parents. Sanger sequencing verified homozygosity of the mutation in the proband and his affected sibling. The autosomal recessive inheritance pattern was confirmed since Sanger sequencing revealed both healthy parents were heterozygous for the mutation. PolyPhen2, SIFT, PROVEAN, and CADD were used to evaluate the function prediction scores of detected mutations. Cx47 is essential for oligodendrocyte function, including adequate myelination and myelin maintenance in humans. Novel mutation p.Val254Met is located in the second extracellular domain of Cx47, both extracellular loops are highly conserved and probably induce intramolecular disulfide interactions. This novel mutation in the Cx47 gene causes oligodendrocyte dysfunction and HLD2 disorder.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.59 no.3
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• pp.263-281
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• 2014

Transcription factors are essential for the regulation of gene expression in plant. They are binding to either enhancer or promoter region of DNA adjacent to the gene and are related to basal transcription regulation, differential enhancement of transcription, development, response to intercellular signals or environment, and cell cycle control. The mechanism in controlling gene expression of transcription can be understood through the assessment of the complete sequence for the maize genome. It is possible that the maize genome encodes 4,000 or more transcription factors because it has undergone whole duplication in the past. Previously, several transcription factors of maize have been characterized. In this review article, the transcription factors were selected using Pfam database, including many family members in comparison with other family and listed as follows: ABI3/VP1, AP2/EREBP, ARF, ARID, AS2, AUX/IAA, BES1, bHLH, bZIP, C2C2-CO-like, C2C2-Dof, C2C2-GATA, C2C2-YABBY, C2H2, E2F/DP, FHA, GARP-ARR-B, GeBP, GRAS, HMG, HSF, MADS, MYB, MYB-related, NAC, PHD, and WRKY family. For analyzing motifs, each amino acid sequence has been aligned with ClustalW and the conserved sequence was shown by sequence logo. This review article will contribute to further study of molecular biological analysis and breeding using the transcription factor of maize as a strategy for selecting target gene.

• Korean Journal of Microbiology
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• v.54 no.3
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• pp.286-288
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• 2018

Moraxella osloensis NP7 was isolated from human skin of a collage male and showed resistance to ${\beta}-lactam$ and aminoglycoside antibiotics. Herein, we report the complete whole-genome sequence and gene annotations of M. osloensis NP7. It possesses single circular chromosome and seven plasmids. Chromosome is 2,389,582 bp in length with the G + C content of 43.9% and encodes 2,065 protein-coding genes. The combined seven plasmids are 654,202 bp in size with the average G + C content of 40.5% and code for a total of 667 protein-coding genes. The chromosome of NP7 strain contains four ribosomal RNA operon copies, one transfer-messenger RNA gene, forty-seven tRNA genes, three riboswitch genes and three CRISPR arrays. Additional CRISPR array is found in the plasmid pNP7-1. The genes conferring resistance to ${\beta}-lactam$ and aminoglycoside antibiotics were predicted to reside in the plasmid pNP7-1.

• Molecules and Cells
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• v.27 no.4
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• pp.459-465
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• 2009

MUG1 is a MULE transposon-related domesticated gene in plants. We assessed the sequence diversity, neutrality, expression, and phylogenetics of the MUG1 gene among Oryza ssp. We found MUG1 expression in all tissues analyzed, with different levels in O. sativa. There were 408 variation sites in the 3886 bp of MUG1 locus. The nucleotide diversity of the MUG1 was higher than functionally known genes in rice. The nucleotide diversity (${\pi}$) in the domains was lower than the average nucleotide diversity in whole coding region. The ${\pi}$ values in nonsynonymous sites were lower than those of synonymous sites. Tajima D and Fu and Li $D^*$ values were mostly negative values, suggesting purifying selection in MUG1 sequences of Oryza ssp. Genome-specific variation and phylogenetic analyses show a general grouping of MUG1 sequences congruent with Oryza ssp. biogeography; however, our MUG1 phylogenetic results, in combination with separate B and D genome studies, might suggest an early divergence of the Oryza ssp. by continental drift of Gondwanaland. O. long-istaminata MUG1 divergence from other AA diploids suggests that it might not be a direct ancestor of the African rice species.

• Journal of Life Science
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• v.26 no.7
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• pp.855-867
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• 2016

The horse is relatively earlier domesticated animal species. Domesticated horses have been selected for their ability of racing, robustness, and disease-resistance. As a result, the thoroughbred horse genome has been condensed many genotypes related to exercise ability. In recent years, with the advent of NGS technologies, many studies were concentrated on finding superior genetic species in the horse genome in terms of genomics. Consequently, GWAS (Genome-wide Association study) is applied to horse genome, then genetic marker is revealed for superior racing ability. In addition, RNA-Seq is utilized as a method for analyze of whole transcript profiling in specific samples. By using this approach, specific gene expression patterns and transcript sequences can be revealed in various samples such as each individual, before and after exercise state, and each tissue. DNA methylation, a strong factor that regulate gene expression without the change of DNA sequence, have got a lot of attention. In horse genome, exercise- or individual-specific DNA methylation patterns were detected, and could be useful to develop selective marker of superior horses. MicroRNAs inhibit gene expression, and transposable elements accounted for half of the mammalian genome. These two elements are the crucial factors in functional genomics, and could be applied to the selection of superior horses. As the functional genomics and epigenomics advance, then these technologies introduced in this paper were applied to select superior horses. In this paper, the studies for selection of superior horses through genetic technologies, and development possibilities of these studies were discussed.

• Mycobiology
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• v.50 no.1
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• pp.66-78
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• 2022

The identification of oleaginous yeast species capable of simultaneously utilizing xylose and glucose as substrates to generate value-added biological products is an area of key economic interest. We have previously demonstrated that the Cutaneotrichosporon dermatis NICC30027 yeast strain is capable of simultaneously assimilating both xylose and glucose, resulting in considerable lipid accumulation. However, as no high-quality genome sequencing data or associated annotations for this strain are available at present, it remains challenging to study the metabolic mechanisms underlying this phenotype. Herein, we report a 39,305,439 bp draft genome assembly for C. dermatis NICC30027 comprised of 37 scaffolds, with 60.15% GC content. Within this genome, we identified 524 tRNAs, 142 sRNAs, 53 miRNAs, 28 snRNAs, and eight rRNA clusters. Moreover, repeat sequences totaling 1,032,129 bp in length were identified (2.63% of the genome), as were 14,238 unigenes that were 1,789.35 bp in length on average (64.82% of the genome). The NCBI non-redundant protein sequences (NR) database was employed to successfully annotate 11,795 of these unigenes, while 3,621 and 11,902 were annotated with the Swiss-Prot and TrEMBL databases, respectively. Unigenes were additionally subjected to pathway enrichment analyses using the Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Cluster of Orthologous Groups of proteins (COG), Clusters of orthologous groups for eukaryotic complete genomes (KOG), and Non-supervised Orthologous Groups (eggNOG) databases. Together, these results provide a foundation for future studies aimed at clarifying the mechanistic basis for the ability of C. dermatis NICC30027 to simultaneously utilize glucose and xylose to synthesize lipids.