• Genomics & Informatics
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• v.4 no.4
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• pp.182-187
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• 2006

6-Phosphogluconolactonase (6PGL) is one of the key enzymes in the ubiquitous pathways of central carbon metabolism, but bacterial 6PGL had been long known as a missing enzyme even after complete bacterial genome sequence information became available. Although recent experimental characterization suggests that there are two types of 6PGLs (DevB and YbhE), their phylogenetic distribution is severely biased. Here we present that proteins in COG group previously described as 3-oarboxymuconate cyclase (COG2706) are actually the YbhE-type 6PGLs, which are widely distributed in Proteobacteria and Fimicutes. This case exemplifies how erroneous functional description of a member in the reference database commonly used in transitive genome annotation cause systematic problem in the prediction of genes even with universal cellular functions.

• Korean Journal of Plant Taxonomy
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• v.46 no.1
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• pp.60-64
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• 2016

Scopolia parviflora of the family Solanaceae is an endemic species of Korea and a traditional Korean medicinal plant. The plastid genome was sequenced by next-generation sequencing (NGS) method. The characterized cp genome is 156,193 bp in size; the large single-copy (LSC) region is 86,364 bp, the inverted repeat (IR) is 25,905 bp, and the small single copy (SSC) region is 18,019 bp. The overall GC content of the plastid genome amounts to 37.61%. The cp genome contains 113 genes and 21 introns, including 80 proteincoding genes, four RNA genes, 30 tRNA genes, 20 group II introns, and one group I intron. A phylogenetic analysis showed that Scopolia parviflora was closely related to Hyoscyamus niger.

• Journal of Animal Science and Technology
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• v.62 no.6
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• pp.952-955
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• 2020

Bacteroides sp. CACC 737 was isolated from a feline, and its potential probiotic properties were characterized using functional genome analysis. Whole-genome sequencing was performed using the PacBio RSII and Illumina HiSeq platforms. The complete genome of strain CACC 737 contained 4.6 Mb, with a guanine (G) + cytosine (C) content of 45.8%, six cryptic plasmids, and extracellular polysaccharide gene as unique features. The strain was beneficial to animal health when consumed as feed, for example, for ameliorating immunological dysfunctions and metabolic disorders. The genome information adds to the comprehensive understanding of Bacteroides sp. and suggests potential animal-related industrial applications for this strain.

• BMB Reports
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• v.49 no.12
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• pp.653-654
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• 2016

The human reference genome, maintained by the Genome Reference Consortium, is conceivably the most complete genome assembly ever, since its first construction. It has continually been improved by incorporating corrections made to the previous assemblies, thanks to various technological advances. Many currently-ongoing population sequencing projects have been based on this reference genome, heightening hopes of the development of useful medical applications of genomic information, thanks to the recent maturation of high-throughput sequencing technologies. However, just one reference genome does not fit all the populations across the globe, because of the large diversity in genomic structures and technical limitations inherent to short read sequencing methods. The recent success in de novo construction of the highly contiguous Asian diploid genome AK1, by combining single molecule technologies with routine sequencing data without resorting to traditional clone-by-clone sequencing and physical mapping, reveals the nature of genomic structure variation by detecting thousands of novel structural variations and by finally filling in some of the prior gaps which had persistently remained in the current human reference genome. Now it is expected that the AK1 genome, soon to be paired with more upcoming de novo assembled genomes, will provide a chance to explore what it is really like to use ancestry-specific reference genomes instead of hg19/hg38 for population genomics. This is a major step towards the furthering of genetically-based precision medicine.

• Korean Journal of Microbiology
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• v.55 no.2
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• pp.171-173
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• 2019

The genus Cohnella, which belongs to the family Paenibacillaceae, inhabits a wide range of environmental niches. Here, we report the complete genome sequence of Cohnella sp. HS21, which was isolated from the rhizospheric soil of Korean fir (Abies koreana) on the top of Halla Mountain in the Republic of Korea. Strain HS21 features a 7,059,027 bp circular chromosome with 44.8% GC-content. Its genome contains 5,939 protein-coding genes, 78 transfer RNA (tRNA) genes, 27 ribosomal RNA (rRNA) genes, 4 noncoding RNA genes (ncRNA), and 90 pseudogenes. The bacterium contains antibiotic-related gene clusters and genes encoding plant cell wall-degrading enzymes.

• Korean Journal of Microbiology
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• v.55 no.3
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• pp.303-305
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• 2019

An actinobacterial strain designated Gordonia sp. MMS17-SY073 (=KCTC 49257) was isolated from a coastal soil of an island, and its complete genome was analyzed. A single contig consisting of 5,962,176 bp with the G + C content of 67.4% was obtained, and the annotation resulted in 5,201 protein-coding genes, 6 rRNA genes and 45 tRNA genes. Strain MMS17-SY073 was closest to the type strain of Gordonia soli based on the 16S rRNA gene sequence comparison, sharing 98.5% sequence similarity. A number of biosynthetic gene clusters for secondary metabolites, non-ribosomal peptide synthetase types in particular, could be identified from the genome.

• 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.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.49 no.6
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• pp.867-874
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• 2016

Although shrimps belonging to family Crangonidae are known to be genetically divergent and ecologically important among the various benthos, any of their mitochondrial genome has not been reported yet. We here determined the complete mitochondrial genome sequence of Crangon hakodatei (Rathbun, 1902), which was collected from East China Sea ($124^{\circ}E$ and $34.5^{\circ}N$). Total mitochondrial genome length of C. hakodatei was 16,060 bp, in which 13 proteins, 2 ribosomal RNAs, 22 transfer RNAs and a putative control region were encoded. Secondary structure prediction analysis showed that twenty tRNA genes exhibit the conserved structure but two genes, $tRNA^{Cys}$ and $tRNA^{Ser}$ (AGN), lack T and D arm, respectively. Based on the sequence similarity of the COI region from the currently reported five species belonging to genus Crangonidae, C. hakodatei was most closely related to Crangon crangon. Phylogenetic analysis of full COXI genes belonging to infraorder Caridea showed that only crangonid shrimps were clustered together with those of Dendrobranchiata. Gene order were well conserved from Penaeoidea to Caridea but $tRNA^{Pro}$ and $tRNA^{Thr}$ in Palaemonid shrimp were flipped each other by the recombination. Further study about mitochondrial genome sequences of shrimps belonging to Crangonidae should be made to know better about their evolutional relationships with other those in infraorder Caridea.

• Korean Journal of Microbiology
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• v.54 no.2
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• pp.155-157
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• 2018

Salmonella enterica subsp. enterica serovar Thompson strain MFDS1004024 was isolated from crab-stick in Korean food-borne outbreak in 2014. Here, we present the complete genome sequence of strain MFDS1004024 with a size of 4,742,942 bp and a mean G + C content of 52%. The genome included 4,373 coding sequences, and 22 ribosomal RNA and 84 transfer RNA genes. Also, we found that strain MFDS1004024 has some genes for Salmonella infection and beta-lactam resistance in its genome based on the result of genome analysis.

• Ocean and Polar Research
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• v.43 no.4
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• pp.371-374
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• 2021

Triglopsis quadricornis Linnaeus, 1758 (Cottidae) is distributed in the Atlantic and Arctic and has four unique bony protuberances on its head. Here, we report the complete, circular, and annotated mitochondrial genome of T. quadricornis. The complete T. quadricornis mitochondrion was sequenced by high-throughput Illumina HiSeq platform. The sequences are 16,736 bp in size and contains 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, a control region, and large and small ribosomal subunits. The overall genomic structure of T. quadricornis mitochondrion was conserved with the gene arrangement of Megalocottus and Myoxocephalus species, and phylogenetic analysis supports their sister relationships. Most PCGs consist of TAA or TAG as a termination codon, whereas COII, ND4, and CYTB have T-- as a stop codon. This complete mitochondrial DNA information of T. quadricornis will provide an essential genomic resource to elucidate the phylogenetic relationship and evolutionary history of the family Cottidae.