• Animal Systematics, Evolution and Diversity
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• v.36 no.4
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• pp.336-346
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• 2020

Mitochondrial genome is an important molecule for systematic and evolutionary studies in metazoans. The development of next-generation sequencing (NGS) technique has rapidly increased the number of mitogenome sequences. The process of generating mitochondrial genome based on NGS includes different steps, from DNA preparation, sequencing, assembly, and annotation. Despite the effort to improve sequencing, assembly, and annotation methods of mitogenome, the low quality and/or quantity sequence in the final map can still be generated through the work. Therefore, it is necessary to check and curate mitochondrial genome sequence after annotation for proofreading and feedback. In this study, we introduce the pipeline for sequencing and curation for mitogenome based on NGS. For this purpose, two mitogenome sequences of Dermatobranchus otome were sequenced by Illumina Miseq system with different amount of raw read data. Generated reads were targeted for assembly and annotation with commonly used programs. As abnormal repeat regions present in the mitogenomes after annotation, primers covering these regions were designed and conventional PCR followed by Sanger sequencing were performed to curate the mitogenome sequences. The obtained sequences were used to replace the abnormal region. Following the replacement, each mitochondrial genome was compared with the other as well as the sequences of close species available on the Genbank for confirmation. After curation, two mitogenomes of D. otome showed a typically circular molecule with 14,559 bp in size and contained 13 protein-coding genes, 22 tRNA genes, two rRNA genes. The phylogenetic tree revealed a close relationship between D. otome and Tritonia diomea. The finding of this study indicated the importance of caution and curation for the generation of mitogenome from NGS.

• Journal of Animal Science and Technology
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• v.63 no.6
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• pp.1411-1422
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• 2021

Lactobacillus acidophilus is a gram-positive, microaerophilic, and acidophilic bacterial species. L. acidophilus strains in the gastrointestinal tracts of humans and other animals have been profiled, but strains found in the canine gut have not been studied yet. Our study helps in understanding the genetic features of the L. acidophilus C5 strain found in the canine gut, determining its adaptive features evolved to survive in the canine gut environment, and in elucidating its probiotic functions. To examine the canine L. acidophilus C5 genome, we isolated the C5 strain from a Korean dog and sequenced it using PacBio SMRT sequencing technology. A comparative genomic approach was used to assess genetic relationships between C5 and six other strains and study the distinguishing features related to different hosts. We found that most genes in the C5 strain were related to carbohydrate transport and metabolism. The pan-genome of seven L. acidophilus strains contained 2,254 gene families, and the core genome contained 1,726 gene families. The phylogenetic tree of the core genes in the canine L. acidophilus C5 strain was very close to that of two strains (DSM20079 and NCFM) from humans. We identified 30 evolutionarily accelerated genes in the L. acidophilus C5 strain in the ratio of non-synonymous to synonymous substitutions (dN/dS) analysis. Five of these thirty genes were associated with carbohydrate transport and metabolism. This study provides insights into genetic features and adaptations of the L. acidophilus C5 strain to survive the canine intestinal environment. It also suggests that the evolution of the L. acidophilus genome is closely related to the host's evolutionary adaptation process.

• Genomics & Informatics
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• v.20 no.3
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• pp.35.1-35.9
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• 2022

Microsatellites or simple sequence repeats are motifs of 1 to 6 nucleotides in length present in both coding and non-coding regions of DNA. These are found widely distributed in the whole genome of prokaryotes, eukaryotes, bacteria, and viruses and are used as molecular markers in studying DNA variations, gene regulation, genetic diversity and evolutionary studies, etc. However, in vitro microsatellite identification proves to be time-consuming and expensive. Therefore, the present research has been focused on using an in-house built java pipeline to identify, analyse, design primers and find related statistics of perfect and compound microsatellites in the seven complete genome sequences of coronavirus, including the genome of coronavirus disease 2019, where the host is Homo sapiens. Based on search criteria among seven genomic sequences, it was revealed that the total number of perfect simple sequence repeats (SSRs) found to be in the range of 76 to 118 and compound SSRs from 01 to10, thus reflecting the low conversion of perfect simple sequence to compound repeats. Furthermore, the incidence of SSRs was insignificant but positively correlated with genome size (R² = 0.45, p > 0.05), with simple sequence repeats relative abundance (R² = 0.18, p > 0.05) and relative density (R² = 0.23, p > 0.05). Dinucleotide repeats were the most abundant in the coding region of the genome, followed by tri, mono, and tetra. This comparative study would help us understand the evolutionary relationship, genetic diversity, and hypervariability in minimal time and cost.

• Journal of Species Research
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• v.13 no.2
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• pp.127-130
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• 2024

The first complete mitogenome sequence of the Red-tongue Pit Viper (Gloydius ussuriensis) from Korea was characterized using next-generation sequencing. The mitogenome is a circular molecule (17,209 bp) with a typical vertebrate mitogenome arrangement, which consists of 2 ribosomal RNA genes (rRNA), 22 transfer RNA genes (tRNA), two non-coding regions (D-loop), and 13 protein-coding genes (PCGs). The base composition of the mitogenome is 32.7% of A, 27.5% of C, 13.9% of G, and 25.9% of T, with a slight AT bias(58.6%). This phylogenetic analysis infers that G. ussuriensis is in the same group as the Chinese G. ussuriensis (Accession No. KP262412) and is closely related to G. blomhoffi and other species of the genus Gloydius. In our study, the complete mitogenome sequence of Korean G. ussuriensis was characterized and we provided basic genetic information on this species.

• Proceedings of the Korean Society of Life Science Conference
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• 2000.06a
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• pp.3-8
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• 2000

The complete genome sequence of a Gram-positive bacterium .Bacillus subtilis has recently been reported and it is now clear that more than 50% of its ORFs have no known function (1). To study the global gene expression in B. subtilis at single gene resolution, we have tested the glass DNA microarrays in a step-wise fashion. As a preliminary experiment, we have created arrays of PCR products for 14 ORF whose transcription patterns have been well established through transcriptional mapping analysis. We measured changes in mRNA transcript levels between early exponential and stationary phase by hybridizing fluorescently labeled cDNA (with Cy3-UTP and Cy5-UTP) onto the array. We then compared the microarray data to confirm that the transcription patterns of these genes are well consistent with the known Northern analysis data. Since the preliminary test has been successful, we scaled up the experiments to ${\sim}$94% of the 4,100 annotated ORFs for the complete genome sequence of B. subtilis. Using this whole genomic microarray, we searched genes that are catabolite-repressive and those that are under the control of ${\sigma}^{Y}$, one of the functionally unknown ECF sigma factors. From these results, we here report that we have established DNA microarray techniques that are applicable for the whole genome of B. subtilis.

• Korean Journal of Microbiology
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• v.55 no.2
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• pp.154-156
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• 2019

Eikenella corrodens is Gram-negative, facultatively anaerobic, and rod-shaped bacterium. It is a part of the normal human mucosal flora that can cause several systemic diseases such as endocarditis, liver abscess, and intracranial bacterial infection. E. corrodens KCOM 3110 (= JS217) was isolated from human subgingival dental plaque of periodontitis lesion. Here, we present the complete genome sequence of E. corrodens KCOM 3110.

• Research in Plant Disease
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• v.24 no.4
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• pp.276-284
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• 2018

In 2010, foliar symptoms were observed in the paprika leaves in Jinju city, Korea. Beet western yellows virus (BWYV) was identified in paprika by using the large-scale oligonucleotide chip assay. To investigate the occurrence of BWYV, a survey was performed on various crops, including paprika, from 2011 to 2014. Further, the presence of BWYV was consistently verified through literature survey from 2015 to 2017. BWYV infection has been identified in Solanaceae crops (bell pepper, hot pepper, and paprika), various weeds, and green peach aphids and it occurs on a nationwide scale. Cultivation using organic methods involved natural enemies and showed a high BWYV infection rate, which was more than that for conventional cultivation methods in greenhouse. The complete genome sequence of BWYV isolated from paprika was determined for the first time. The genome of the BWYV-Korea isolate consists of 5750 nucleotides and has six open reading frames. Sequence identity results showed maximum similarity between the BWYV-Korea isolate and the BWYV LS isolate (identity > 90%). This study is the first report of BWYV infecting paprika in Korea. The survey revealed that BWYV is naturalized in the domestic ecology of Korea.

• Korean Journal of Microbiology
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• v.54 no.4
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• pp.471-473
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• 2018

Variovorax sp. PMC12 is a rhizobacterium isolated from tomato rhizosphere and enhanced the plant resistance to abiotic and biotic stresses. Here we present the complete genome sequence of strain PMC12. The genome is comprised of two circular chromosomes harboring 5,873,297 bp and 1,141,940 bp, respectively. A total of 6,436 protein-coding genes, 9 rRNAs, 64 tRNAs, 3 ncRNAs, and 80 pseudogenes were identified. We found genes involved in 1-aminocyclopropane-1-carboxylate (ACC) deaminase, antioxidant activity, phosphate solubilization, and biosynthesis of proline and siderophore. Those genes may be related to capability of improving plant resistance to various stresses including salinity, cold temperature, and phytopathogen.

• 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.

• Microbiology and Biotechnology Letters
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• v.52 no.1
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• pp.102-104
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• 2024

Massilia sp. KACC 81254BP, isolated from a landfill on Jeju Island, Republic of Korea, possesses the capability to degrade polyhydroxyalkanoates (PHAs). The genomic analysis of strain KACC 81254BP consists of a circular chromosome comprising 5,028,452 base pairs with a DNA G+C content of 64.6%. This complete genome consists of a total of 4,513 genes, including those encoding the PHA degradation enzyme (PhaZ). This study offers valuable genomic insights into the enzymes responsible for degrading polyester plastics.