• Genomics & Informatics
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• v.5 no.4
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• pp.152-160
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• 2007

Most common diseases are caused by multiple genetic and environmental factors. Among the genetic factors, single nucleotide polymorphisms (SNPs) are common DNA sequence variations in individuals and can serve as important genetic markers. Recently, investigations of gene-based and whole genome-based SNPs have been applied to association studies for marker discovery. However, SNPs are so population-specific that the association needs to be verified. Fifty-five genes and 384 SNPs were selected based on association with disease. Genotypes of 337 SNPs in candidate genes were determined using Illumina Sentrix Array Matrix (SAM) chips by an allele-specific extension method in 364 unrelated Korean individuals. Allelic frequencies of SNPs were compared with those of other populations obtained from the International HapMap database. Minor allele frequencies, linkage disequilibrium blocks, tagSNPs, and haplotypes of functional candidate SNPs in 55 genetic disease-associated genes were provided. Our data may provide useful information for the selection of genetic markers for gene-based genetic disease-association studies of the Korean population.

• Journal of Animal Science and Technology
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• v.63 no.5
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• pp.1207-1210
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• 2021

Lactobacillus amylovorus are known to exist in the intestinal flora of healthy cattle or pigs. The L. amylovorus strain 1394N20 was isolated from the feces of the Hanwoo calf (Bos taurus coreanae). The genome of strain 1394N20 consists of a single circular chromosome (2,176,326 bp) with overall guanine + cytosine content of 37.8 mol%. Moreover, 2,281 protein-coding sequences, 15 rRNAs, and 65 tRNAs genes were identified in the chromosome based on the results of annotation. The bacterium has a gene encoding endoglucanase, an enzyme that hydrolyzes the 1,4-β-D-glycosidic linkages in cellulose, hemicellulose, lichenin, and cereal β-D-glucans. Genomic sequencing of L. amylovorus strain 1394N20 reveals the immense potential of the strain as a probiotic with nutrient digestibility.

• Journal of Food Hygiene and Safety
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• v.39 no.3
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• pp.231-238
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• 2024

Vibrio parahaemolyticus is a major seafood-borne pathogen commonly detected in marine environments. In Korea, V. parahaemolyticus-induced foodborne illnesses account for 7.5% of bacterial pathogen-related food poisonings. Moreover, the amount of antimicrobial agents used in aquatic cultures is continuously increasing. In this study, we isolated V. parahaemolyticus from seafood samples and performed antimicrobial susceptibility tests using the microbroth dilution method. Furthermore, using whole-genome sequencing, we identified antimicrobial resistance genes, virulence genes, and sequence types (STs). We could isolate V. parahaemolyticus from 47 (59.5%) of the 79 seafood samples we purchased from retail markets in Seoul and Chungcheong provinces. Antimicrobial susceptibility tests revealed that 2 and all of the 47 isolates were ampicillin-resistant (4.3%) and susceptible to all tested antimicrobial agents (100%), respectively. The genotype analysis revealed that all isolates carried beta-lactam-, tetracycline-, and chloramphenicol-associated antimicrobial resistance genes. However, we could detect fosfomycin resistance only in one isolate. Concerning the virulence genes, we detected T3SS1 and T3SS2-associated genes in all and one isolate, respectively. However, we could not detect the tdh and trh genes. Of the 47 isolates, 17 belonged to 15 different STs, including ST 658 with 3 isolates. The rest 30 isolates were identified as 25 new STs. The results of this study support the need for operating a continuous monitoring system to prevent foodborne illnesses and the spread of antimicrobial resistance genes in V. parahaemolyticus.

• Asian-Australasian Journal of Animal Sciences
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• v.32 no.4
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• pp.494-500
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• 2019

Objective: Feed consumption contributes a large percentage for total production costs in the poultry industry. Detecting genes associated with feeding traits will be of benefit to improve our understanding of the molecular determinants for feed efficiency. The objective of this study was to identify candidate genes associated with feed conversion ratio (FCR) via genomewide association study (GWAS) using sequence data imputed from single nucleotide polymorphism (SNP) panel in a Chinese indigenous chicken population. Methods: A total of 435 Chinese indigenous chickens were phenotyped for FCR and were genotyped using a 600K SNP genotyping array. Twenty-four birds were selected for sequencing, and the 600K SNP panel data were imputed to whole sequence data with the 24 birds as the reference. The GWAS were performed with GEMMA software. Results: After quality control, 8,626,020 SNPs were used for sequence based GWAS, in which ten significant genomic regions were detected to be associated with FCR. Ten candidate genes, ubiquitin specific peptidase 44, leukotriene A4 hydrolase, ETS transcription factor, R-spondin 2, inhibitor of apoptosis protein 3, sosondowah ankyrin repeat domain family member D, calmodulin regulated spectrin associated protein family member 2, zinc finger and BTB domain containing 41, potassium sodium-activated channel subfamily T member 2, and member of RAS oncogene family were annotated. Several of them were within or near the reported FCR quantitative trait loci, and others were newly reported. Conclusion: Results from this study provide valuable prior information on chicken genomic breeding programs, and potentially improve our understanding of the molecular mechanism for feeding traits.

• 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.

• Asian-Australasian Journal of Animal Sciences
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• v.31 no.12
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• pp.1980-1990
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• 2018

Objective: The aim of this study was to discover the functional impact of non-synonymous single nucleotide polymorphisms (nsSNPs) that were found in selective sweep regions of the Landrace genome Methods: Whole-genome re-sequencing data were obtained from 40 pigs, including 14 Landrace, 16 Yorkshire, and 10 wild boars, which were generated with the Illumina HiSeq 2000 platform. The nsSNPs in the selective sweep regions of the Landrace genome were identified, and the impacts of these variations on protein function were predicted to reveal their potential association with traits of the Landrace breed, such as reproductive capacity. Results: Total of 53,998 nsSNPs in the mapped regions of pigs were identified, and among them, 345 nsSNPs were found in the selective sweep regions of the Landrace genome which were reported previously. The genes featuring these nsSNPs fell into various functional categories, such as reproductive capacity or growth and development during the perinatal period. The impacts of amino acid sequence changes by nsSNPs on protein function were predicted using two in silico SNP prediction algorithms, i.e., sorting intolerant from tolerant and polymorphism phenotyping v2, to reveal their potential roles in biological processes that might be associated with the reproductive capacity of the Landrace breed. Conclusion: The findings elucidated the domestication history of the Landrace breed and illustrated how Landrace domestication led to patterns of genetic variation related to superior reproductive capacity. Our novel findings will help understand the process of Landrace domestication at the genome level and provide SNPs that are informative for breeding.

• International Journal of Industrial Entomology and Biomaterials
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• v.44 no.2
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• pp.55-64
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• 2022

Bombyx shini Park & Sohn, 2002 (Lepidoptera: Bombycidae), which was listed as an endemic species in South Korea has recently been renamed as the East Asian silk moth Rotunda rotundapex Miyata & Kishida, 1990 (Lepidoptera: Bombycidae). In this study, we sequenced the complete mitochondrial genome (mitogenome) of the R. rotundapex to announce genomic characteristics and to clarify its validity with a new name. The 15,294-bp long complete mitogenome comprises a typical set of genes [13 protein-coding genes (PCGs), 2 rRNA genes, and 22 tRNA genes] and one major noncoding, A + T-rich region, with an arrangement identical to that observed in most lepidopteran mitogenomes. The A/T content of the whole mitogenome was 79.22%; however, it varied among the regions/genes as follows: A + T-rich region, 91.62%; srRNA, 84.67%; lrRNA, 83.01%; tRNAs, 81.43%; and PCGs, 77.46%. Phylogenetic analyses of 35 species in the Bombycoidea superfamily showed the sister relationship between the families Sphingidae and Bombycidae s. str., with the higher nodal support [bootstrap support (BS) = 78%]. The Saturniidae was placed as the sister to the two families, but the nodal support for this relationship was low (BS = 53%). Current R. rotundapex was placed together with previously reported con-species with the highest nodal support, forming a separate clade from Bombyx, validating that B. shini can have a new genus name, Rotunda. However, the Korean R. rotundapex showed a substantial sequence divergence at 5.28% to that originated from an individual of type locality Taiwan in 1,459-bp of COI sequences. Considering such a high sequence divergence an additional study, which includes morphological and DNA barcoding data from further extensive distributional range maybe is needed for further robust taxonomic conclusion.

• Journal of Veterinary Science
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• v.23 no.5
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• pp.67.1-67.11
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• 2022

Background: Budgerigar fledgling disease polyomavirus (BFDV) is the pathogen that causes budgerigar fledgling disease in psittacine species. The clinical signs of PBFV infection include ascites, hepatitis, and crop stasis. BFDV is associated with a high mortality rate in nestling birds. In contrast, adult birds only have mild symptoms such as feather dystrophy. Objectives: This study aimed to determine the prevalence, genetic characteristics, and phylogenetic analysis of BFDV in pet parrots in Korea. Methods: Fecal and tissue samples were collected from 217 pet parrots from 10 veterinary hospitals including Chungbuk National University Veterinary Hospital. The molecular screening was performed using polymerase chain reaction (PCR) analysis of the small t/large T antigen gene segment. Full-length genome sequencing with the Sanger and phylogenetic analysis were performed on BFDV-positive samples. Results: The PCR results based on the small t/large T antigen gene marker indicated that BFDV DNA was present in 10 out of 217 screened samples. A whole-genome sequence was obtained from six strains and phylogenetic analysis revealed no significant relationship existed between the species and geographical locations amongst them. Conclusions: The prevalence of BFDV infection in South Korea is not high when compared to the prevalence of BFDV in other parts of the world, however, it has been reported sporadically in various species and geographic locations. The whole-genome analysis revealed 0.2%-0.3% variation in intragenomic homogeneity among the six strains analyzed. Korean strains are separately on the phylogenetic tree from their counterparts from China and Japan which might reflect the substantial genetic variation.

• The Journal of the Korea Contents Association
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• v.22 no.2
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• pp.762-769
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• 2022

Genetic testing in prenatal diagnosis is a precious tool providing valuable information in clinical management and parental decision-making. For the last year, cytogenetic testing methods, such as G-banding karyotype analysis, fluorescent in situ hybridization, chromosomal microarray, and gene panels have evolved to become part of routine laboratory testing. However, the limitations of each of these methods demonstrate the need for a revolutionary technology that can alleviate the need for multiple technologies. The recent introduction of new genomic technologies based on next-generation sequencing has changed the current practice of prenatal testing. The promise of these innovations lies in the fast and cost-effective generation of genome-scale sequence data with exquisite resolution and accuracy for prenatal diagnosis. Here, we review the current state of sequencing-based pediatric diagnostics, associated challenges, as well as future prospects.

• The Plant Pathology Journal
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• v.39 no.4
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• pp.409-416
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• 2023

Bacterial leaf blight of carrots caused by Xanthomonas hortorum pv. carotae (Xhc) is an important worldwide seed-borne disease. In 2012 and 2013, symptoms similar to bacterial leaf blight were found in carrot farms in Jeju Island, Korea. The phenotypic characteristics of the Korean isolation strains were similar to the type strain of Xhc. Pathogenicity showed symptoms on the 14th day after inoculation on carrot plants. Identification by genetic method was multi-position sequencing of the isolated strain JJ2001 was performed using four genes (danK, gyrB, fyuA, and rpoD). The isolated strain was confirmed to be most similar to Xhc M081. Furthermore, in order to analyze the genetic characteristics of the isolated strain, whole genome analysis was performed through the next-generation sequencing method. The draft genome size of JJ2001 is 5,443,372 bp, which contains 63.57% of G + C and has 4,547 open reading frames. Specifically, the classification of pathovar can be confirmed to be similar to that of the host lineage. Plant pathogenic factors and determinants of the majority of the secretion system are conserved in strain JJ2001. This genetic information enables detailed comparative analysis in the pathovar stage of pathogenic bacteria. Furthermore, these findings provide basic data for the distribution and diagnosis of Xanthomonas hortorum pv. carotae, a major plant pathogen that infects carrots in Korea.