• Journal of Microbiology and Biotechnology
• /
• v.10 no.6
• /
• pp.823-828
• /
• 2000

The complete nucleotide sequence of hepatitis B virus DNA isolated from Korean patient serum was determined and characterized, and its phylogenetic relation was then investigated. The viral genome was 3,215 base pairs long and included four well known open reading frames (i.e. surface antigens, core antigens, X protein and DNA polymerase). The sequence of the surface antigen showed that the HBV genome under investigation, designated HBV 315, was characteristic of subtype adr. A phylogenetic analysis using the total genome sequence revealed that HBV315 was grouped into genomic group C together with isolates from Japan, China, Thailand, Polynesia, and New Caledonia. The mean percent similarity between HBV315 and other HBV isolates in genomic group C was 97.25%, and that with other genomic groups ranged from 86.16% to 91.25%. The predicted amino acid sequences of HBV315 were compared with two closely related subtype adr isolates, M38636 and D12980. The results showed that the X gene product was identical in the three strains, while there were significant amino acid sequence differences between HBV315 and M38636 in the Pre-S1 and Pre-S2 regions.

• Proceedings of the Korean Society of Crop Science Conference
• /
• 2022.10a
• /
• pp.270-270
• /
• 2022

• Microbiology and Biotechnology Letters
• /
• v.46 no.2
• /
• pp.162-170
• /
• 2018

Non-typhoidal Salmonella is one of the main pathogens causing food-borne illness in humans, with up to 20% of cases resulting from consumption of pork products. Over the gastroenteritis signs, multidrug resistant Salmonella has arisen. In this study, pan-susceptible phenotypic strains of Salmonella enterica serotype Weltevreden recovered from pig production chain in Chiang Mai, Thailand during 2012-2014 were chosen for analysis. The aim of this study was to use whole genome sequencing (WGS) data with an emphasis on antimicrobial resistance gene investigation to assess their pathogenic potential and genetic diversity determination based on whole genome Multilocus Sequence Typing (wgMLST) to expand epidemiological knowledge and to provide additional guidance for disease control. Analyis using ResFinder 3.0 for WGS database tracing found that one of pan-susceptible phenotypic strain carried five classes of resistance genes: aminoglycoside, beta-lactam, phenicol, sulfonamide, and tetracycline associated genes. Twenty four and 36 loci differences were detected by core genome Multilocus Sequence Typing (cgMLST) and pan genome Multilocus Sequence Typing (pgMLST), respectively, in two matching strains (44/13 vs A543057 and A543056 vs 204/13) initially assigned by conventional MLST and Pulsed-field Gel Electrophoresis (PFGE). One hundread percent discriminant ability can be achieved using the wgMLST technique. WGS is currently the ultimate molecular technique for various in-depth studies. As the findings stated above, a new of "gold standard typing method era" for routine works in genome study is being set.

• Journal of KIISE:Software and Applications
• /
• v.30 no.3_4
• /
• pp.379-387
• /
• 2003

A lot of microbial genome projects have been completed to pour the enormous amount of genomic sequence data. In this context. the problem of identifying promoters in genomic DNA sequences by computational methods has attracted considerable research attention in recent years. In this paper, we propose a new model of prokaryotic core promoter region including the -10 region and transcription initiation site, that is Dependency-Reflecting Decomposition Model (DRDM), which captures the most significant biological dependencies between positions (allowing for non-adjacent as well as adjacent dependencies). DRDM showed a good result of performance test and it will be employed effectively in predicting promoters in long microbial genomic Contigs.

• BMB Reports
• /
• v.37 no.6
• /
• pp.648-656
• /
• 2004

This paper deals with the development of a predictive probabilistic model, a composite dependency-reflecting model (CDRM), which was designed to detect core promoter regions and transcription start sites (TSS) in vertebrate genomic DNA sequences, an issue of some importance for genome annotation. The model actually represents a combination of first-, second-, third- and much higher order or long-range dependencies obtained using the expanded maximal dependency decomposition (EMDD) procedure, which iteratively decomposes data sets into subsets on the basis of dependency degree and patterns inherent in the target promoter region to be modeled. In addition, decomposed subsets are modeled by using a first-order Markov model, allowing the predictive model to reflect dependency between adjacent positions explicitly. In this way, the CDRM allows for potentially complex dependencies between positions in the core promoter region. Such complex dependencies may be closely related to the biological and structural contexts since promoter elements are present in various combinations separated by various distances in the sequence. Thus, CDRM may be appropriate for recognizing core promoter regions and TSSs in vertebrate genomic contig. To demonstrate the effectiveness of our algorithm, we tested it using standardized data and real core promoters, and compared it with some current representative promoter-finding algorithms. The developed algorithm showed better accuracy in terms of specificity and sensitivity than the promoter-finding ones used in performance comparison.

• Journal of Microbiology and Biotechnology
• /
• v.33 no.7
• /
• pp.875-885
• /
• 2023

Volatile organic compounds such as benzene, toluene, ethylbenzene, and isomers of xylenes (BTEX) constitute a group of monoaromatic compounds that are found in petroleum and have been classified as priority pollutants. In this study, based on its newly sequenced genome, we reclassified the previously identified BTEX-degrading thermotolerant strain Ralstonia sp. PHS1 as Cupriavidus cauae PHS1. Also presented are the complete genome sequence of C. cauae PHS1, its annotation, species delineation, and a comparative analysis of the BTEX-degrading gene cluster. Moreover, we cloned and characterized the BTEX-degrading pathway genes in C. cauae PHS1, the BTEX-degrading gene cluster of which consists of two monooxygenases and meta-cleavage genes. A genome-wide investigation of the PHS1 coding sequence and the experimentally confirmed regioselectivity of the toluene monooxygenases and catechol 2,3-dioxygenase allowed us to reconstruct the BTEX degradation pathway. The degradation of BTEX begins with aromatic ring hydroxylation, followed by ring cleavage, and eventually enters the core carbon metabolism. The information provided here on the genome and BTEX-degrading pathway of the thermotolerant strain C. cauae PHS1 could be useful in constructing an efficient production host.

• Animal Bioscience
• /
• v.37 no.3
• /
• pp.461-470
• /
• 2024

Objective: The objective of this study was to investigate the genetic diversity, population structure and whole-genome selection signatures of Luxi cattle to reveal its genomic characteristics in terms of meat and carcass traits, skeletal muscle development, body size, and other traits. Methods: To further analyze the genomic characteristics of Luxi cattle, this study sequenced the whole-genome of 16 individuals from the core conservation farm in Shandong region, and collected 174 published genomes of cattle for conjoint analysis. Furthermore, three different statistics (pi, F_st, and XP-EHH) were used to detect potential positive selection signatures related to selection in Luxi cattle. Moreover, gene ontology and Kyoto encyclopedia of genes and genomes pathway enrichment analyses were performed to reveal the potential biological function of candidate genes harbored in selected regions. Results: The results showed that Luxi cattle had high genomic diversity and low inbreeding levels. Using three complementary methods (pi, F_st, and XP-EHH) to detect the signatures of selection in the Luxi cattle genome, there were 2,941, 2,221 and 1,304 potentially selected genes identified, respectively. Furthermore, there were 45 genes annotated in common overlapping genomic regions covered 0.723 Mb, including PLAG1 zinc finger (PLAG1), dedicator of cytokinesis 3 (DOCK3), ephrin A2 (EFNA2), DAZ associated protein 1 (DAZAP1), Ral GTPase activating protein catalytic subunit alpha 1 (RALGAPA1), mediator complex subunit 13 (MED13), and decaprenyl diphosphate synthase subunit 2 (PDSS2), most of which were enriched in pathways related to muscle growth and differentiation and immunity. Conclusion: In this study, we provided a series of genes associated with important economic traits were found in positive selection regions, and a scientific basis for the scientific conservation and genetic improvement of Luxi cattle.

• Proceedings of the Korean Society of Crop Science Conference
• /
• 2017.06a
• /
• pp.151-151
• /
• 2017

In Asia, rice production has some difficulties with reduction of farm household population and increase of elderly population. As a result, it has resulted in inefficiency and we needs to reduce labor force and improve labor productivity. Direct-seeding in rice could reduce labor and production costs, the area of direct seeding is increasing in japonica rice production in Asia. In direct seedling cultivation competition against weeds is one of most important concern. So, low temperature germinability and mesocotyl elongation should be considered. In this study, we evaluated the mesocotyl length and low temperature germination conducted association analysis using 137 korea core collections. An average length of mesocotyl among 137 core collections was skewed range from 0mm to 43mm. we searched candidate gene around target SNP. Such related traits, genome-wide association study (GWAS) analysis was carried out using GAPIT. Also, average mesocotyl length of 394 korea landrace cultivars was measured ranging from minimum 0 mm to maximum 34mm. 30 out of 394 Korea landrace cultivar conducted re-sequencing, and haplotype analysis of candidate gene. we searched these related resources, which including germination of low temperature and mesocotyl elongation. This could be used for the development of direct-seeding cultivars. The valiated accession of core collection and landrace cultivars will be used development of direct-seedling cultivar in the future.

• Proceedings of the Korean Society of Crop Science Conference
• /
• 2022.10a
• /
• pp.235-235
• /
• 2022

Genome selection is a promising tool for plant and animal breeding, which uses genome-wide molecular marker data to capture large and small effect quantitative trait loci and predict the genetic value of selection candidates. Genomic selection has been shown previously to have higher prediction accuracies than conventional marker-assisted selection (MAS) for quantitative traits. In this study, the prediction accuracy of 10 agricultural traits in the wheat core group with 567 points was compared. We used a cross-validation approach to train and validate prediction accuracy to evaluate the effects of training population size and training model.As for the prediction accuracy according to the model, the prediction accuracy of 0.4 or more was evaluated except for the SVN model among the 6 models (GBLUP, LASSO, BayseA, RKHS, SVN, RF) used in most all traits. For traits such as days to heading and days to maturity, the prediction accuracy was very high, over 0.8. As for the prediction accuracy according to the training group, the prediction accuracy increased as the number of training groups increased in all traits. It was confirmed that the prediction accuracy was different in the training population according to the genetic composition regardless of the number. All training models were verified through 5-fold cross-validation. To verify the prediction ability of the training population of the wheat core collection, we compared the actual phenotype and genomic estimated breeding value using 35 breeding population. In fact, out of 10 individuals with the fastest days to heading, 5 individuals were selected through genomic selection, and 6 individuals were selected through genomic selection out of the 10 individuals with the slowest days to heading. Therefore, we confirmed the possibility of selecting individuals according to traits with only the genotype for a shorter period of time through genomic selection.

• Mycobiology
• /
• v.44 no.2
• /
• pp.105-111
• /
• 2016

Paclitaxel (taxol) has long been used as a potent anticancer agent for the treatment of many cancers. Ever since the fungal species Taxomyces andreanae was first shown to produce taxol in 1993, many endophytic fungal species have been recognized as taxol accumulators. In this study, we analyzed the taxol-producing capacity of different Colletotrichum spp. to determine the distribution of a taxol biosynthetic gene within this genus. Distribution of the taxadiene synthase (TS) gene, which cyclizes geranylgeranyl diphosphate to produce taxadiene, was analyzed in 12 Colletotrichum spp., of which 8 were found to contain the unique skeletal core structure of paclitaxel. However, distribution of the gene was not limited to closely related species. The production of taxol by Colletotrichum dematium, which causes pepper anthracnose, depended on the method in which the fungus was stored, with the highest production being in samples stored under mineral oil. Based on its distribution among Colletotrichum spp., the TS gene was either integrated into or deleted from the bacterial genome in a species-specific manner. In addition to their taxol-producing capacity, the simple genome structure and easy gene manipulation of these endophytic fungal species make them valuable resources for identifying genes in the taxol biosynthetic pathway.