• Journal of Species Research
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• 제10권2호
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• pp.142-153
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• 2021

Algal genomics approaches provide a massive number of genome/transcriptome sequences and reveal the evolutionary history vis-à-vis primary and serial endosymbiosis events that contributed to the biodiversity of photosynthetic eukaryotes in the eukaryote tree of life. In particular, phylogenomic methods using several hundred or thousands of genes have provided new insights into algal taxonomy and systematics. Using this method, many novel insights into algal species diversity and systematics occurred, leading to taxonomic revisions. In addition, horizontal gene transfers (HGTs) of functional genes have been identified in algal genomes that played essential roles in environmental adaptation and genomic diversification. Finally, algal genomics data can be used to address the pangenome, including core genes shared among all isolates and partially shared strain-specific genes. However, some aspects of the pangenome concept (genome variability of intraspecies level) conflict with population genomics concepts, and the issue is closely related to defining species boundaries using genome variability. This review suggests a desirable future direction to merge algal pangenomics and population genomics beyond traditional molecular phylogeny and taxonomy.

• 한국미생물·생명공학회지
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• 제51권3호
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• pp.296-299
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• 2023

We present the complete genome sequence of Priestia aryabhattai strain S2 isolated from the soybean rhizosphere. The genome consists of a single circular chromosome of 5,070,860 bp with a G+C content of 38.3% and 2 plasmids, P1(148,124 bp, GC content 33.3%) and P2 (76,418 bp, GC content 36.5%).

• Interdisciplinary Bio Central
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• 제2권4호
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• pp.13.1-13.8
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• 2010

The National BioResource Project of Japan is a governmental project to promote domestic/international research activities using biological resources. The project has 27 biological resources including three cereal resources. The core center and sub-center which historically collected the cereal resources were selected for each cereal program. These resources are categorized into several different types in the project; germplasm, genetic stocks, genome resources and database information. Contents of rice resources are wild species, local varieties in East and Southwest Asia & wild relatives, MNU-induced chemical mutant lines, marker tester lines, chromosome substitution lines and other experimental lines. Contents of wheat resources are wild strains, cultivated strains, experimental lines, rye wild and cultivated strains; EST clones and full-length cDNA clones. Contents of barley resources are cultivar and experimental lines, core collection, EST/cDNA clones, BAC clones, their filters and superpool DNA. Each resource is accessible from the online database to see the contents and information about the resources. Links to the genome information and genomic tools are also important function of each database. The major contents and some examples are presented here.

• Molecules and Cells
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• 제37권5호
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• pp.372-382
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• 2014

In this study, the chloroplast (cp) genome sequences from three early diverged leptosporangiate ferns were completed and analyzed in order to understand the evolution of the genome of the fern lineages. The complete cp genome sequence of Osmunda cinnamomea (Osmundales) was 142,812 base pairs (bp). The cp genome structure was similar to that of eusporangiate ferns. The gene/intron losses that frequently occurred in the cp genome of leptosporangiate ferns were not found in the cp genome of O. cinnamomea. In addition, putative RNA editing sites in the cp genome were rare in O. cinnamomea, even though the sites were frequently predicted to be present in leptosporangiate ferns. The complete cp genome sequence of Diplopterygium glaucum (Gleicheniales) was 151,007 bp and has a 9.7 kb inversion between the trnL-CAA and trnV-GCA genes when compared to O. cinnamomea. Several repeated sequences were detected around the inversion break points. The complete cp genome sequence of Lygodium japonicum (Schizaeales) was 157,142 bp and a deletion of the rpoC1 intron was detected. This intron loss was shared by all of the studied species of the genus Lygodium. The GC contents and the effective numbers of codons (ENCs) in ferns varied significantly when compared to seed plants. The ENC values of the early diverged leptosporangiate ferns showed intermediate levels between eusporangiate and core leptosporangiate ferns. However, our phylogenetic tree based on all of the cp gene sequences clearly indicated that the cp genome similarity between O. cinnamomea (Osmundales) and eusporangiate ferns are symplesiomorphies, rather than synapomorphies. Therefore, our data is in agreement with the view that Osmundales is a distinct early diverged lineage in the leptosporangiate ferns.

• Mycobiology
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• 제47권4호
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• pp.466-472
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• 2019

For the purpose of protecting the rights of Lentinula edodes breeders, we developed a new simple sequence repeat (SSR) marker set consisting only of genetically independent tetranucleotide or longer core motifs. Using available genome sequences for five L. edodes strains, we designed primers for 13 SSR markers that amplified polymorphic sequences in 20 L. edodes cultivars. We evaluated the independence of every possible marker pair based on genotype data. Consequently, eight genetically independent markers were selected. The polymorphic information content values of the markers ranged from 0.269 to 0.764, with an average of 0.409. The markers could distinguish among 20 L. edodes cultivars and produced highly repeatable and reproducible results. The markers developed in this study will enable the precise identification of L. edodes cultivars, and may be useful for protecting breeders' rights.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2017년도 9th Asian Crop Science Association conference
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• pp.158-158
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• 2017

The purpose of this study was to identify the candidate genes involved in selenium content in brown rice. Rice (Oryza sativa L.) was important crop including diverse functional substance such as carbohydrate, protein, lysine and tocopherol, mineral. Especially, selenium as nutritionally important minerals, it was known to activate the immune system, antioxidant effect and inhibition of carcinogenesis. Also recommended daily requirements of the United States and the United Kingdom were 55 to 90 ug for selenium. Therefore, selenium content in brown rice of core-set were analyzed by using ICP-MS (Inductively Coupled Plasma Mass Spectrometer) and GWAS (Genome Wide Association Study) was conducted to search for candidate genes in this study. The new natural variants identified through haplotyping analysis would be useful to develop new rice varieties with improved storage ability of the valuable mineral through the future molecular breeding.

• 한국미생물생명공학회:학술대회논문집
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• 한국미생물생명공학회 2001년도 Proceedings of 2001 International Symposium
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• pp.15-19
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• 2001

Creating an artificial strain with a minimal gene set for a specific purpose is every biologist's dream. With the complete genome sequencing of more than 50 microorganisms and extensive functional analyses of their genes, it is possible to design a genetic blueprint for a simple custom-designed microbe with the minimal gene set. Two different approaches are being considered. The first 'top-down' approach is trimming the genome to a minimal gene set by selectively removing genes of an organism thought to be unnecessary based on microbial genomics. The second 'bottom-up' approach is to synthesize the proposed minimal genome from basic chemical building blocks. The 'top-down' approach starting with the genome of a well known microorganism is more technically feasible, whereas the bottom-up approach may not be attainable in the nearest future because of the lack of the complete functional analysis of the genes needed for a life. Here in this study, we used the top-down approach to minimize the E. coli genome to create an artificial organism with 'core' elements for self-sustaining and self-replicating cells by eliminating unnecessary genes. Using several different kinds of sophisticated deletion techniques combined with a p:1age and transposons, we deleted about 19％ of the E. coli genome without causing any damages to cellular growth. This smaller E. coli genome will be further reduced to a genome with a minimal gene l;et essential for cell life. This minimized E. coli genome can lead to the construction of many custom-designed strains with myriad practical and commercial applications.

• 한국응용약물학회:학술대회논문집
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• 한국응용약물학회 1994년도 춘계학술대회 and 제3회 신약개발 연구발표회
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• pp.178-178
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• 1994

Hepatitis B Virus (HBV) is a DNA virus with a 3.2kb partially double-stranded genome. The life cycle of the virus involves a reverse transcription of the greater than genome length 3.5kb mRNA. This pegenomic RNA contains all the genetic information encoded by the virus and functions as an intermediate in viral replication. Tumor suppressor p53 has previously been shown to interact with the X-gene product of the HBV, which led us to hypothesize that p53 may act as a negative regulator of HBV replication and the role of the X-gene product is to overcome the p53-mediated restriction. As a first step to prove the above hypothesis, we tested whether p53 represses the propagation of HBV in in vitro replication system. By transient cotransfection of the plasmid containing a complete copy of the HBV genome and/or the plasmid encoding p53, we found that the replication of HBV is specifically blocked by wild-type p53. The levels of HBV DNA, HBs Ag and HBc/e Ag secreted in cell culture media were dramatically reduced upon coexpresion of wild-type p53 but not by the coexpression of the mutants of p53 (G154V and R273L). Furthermore, levels of RNAs originated from HBV genome were repressed more than 10 fold by the cotransfection of the p53 encoding plasmid. These results clearly states that p53 is a nesative regulator of the HBV replication. Next, to addresss the mechanism by which p53 represses the HBV replication, we performed the transient transfection experiments employing the pregenomic/core promoter-CAT(Chloramphenicol Acetyl Transferase) construct as a reporter. Cotransfection of wild-type p53 but not the mutant p53 expression plasmids repressed the CAT activity more than 8 fold. Integrating the above results, we propose that p53 represses the replication of HBV specifically by the down-regulation of the pregenomic/core promoter, which results in the reduced DNA synthesis of HBV. Currently, the mechanism by which HBV overcomes the observed p53-mediated restriction of replication is tinder investigation.

• Genomics & Informatics
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• 제9권4호
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• pp.194-196
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• 2011

Promoter prediction is a very important problem and is closely related to the main problems of bioinformatics such as the construction of gene regulatory networks and gene function annotation. In this context, we developed an integrated promoter prediction program using hybrid methods, PromoterWizard, which can be employed to detect the core promoter region and the transcription start site (TSS) in vertebrate genomic DNA sequences, an issue of obvious importance for genome annotation efforts. PromoterWizard consists of three main modules and two auxiliary modules. The three main modules include CDRM (Composite Dependency Reflecting Model) module, SVM (Support Vector Machine) module, and ICM (Interpolated Context Model) module. The two auxiliary modules are CpG Island Detector and GCPlot that may contribute to improving the predictive accuracy of the three main modules and facilitating human curator to decide on the final annotation.

• Animal cells and systems
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• 제16권3호
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• pp.230-236
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• 2012

The Korean hare, Lepus coreanus, is an important mammal in ecosystem food chains, and is distributed across the entire Korean peninsula and northeastern China. Polymorphic microsatellite loci were developed using the biotinenrichment technique for use in population genetics studies. Five trinucleotide and four dinucleotide microsatellite loci were selected and tested on 22 Korean hare specimens collected from Gangwon Province and Gyeongsangbuk Province in South Korea. The number of alleles across the two sampling regions ranged from three to nine with a mean of 6.1. Mean observed and expected heterozygosities and polymorphic information content were 0.540, 0.627 and 0.579, respectively. Only one locus, Lc06, showed departure from Hardy-Weinberg equilibrium after applying the Bonferroni correction. Four microsatellites, Lc01, Lc03, Lc12, and Lc19, satisfied the criteria to serve as a core set of markers recommended for population genetics studies. These new microsatellite markers will be widely applicable to future genetic studies for management and conservation of the Korean hare and related species, including assessment of the genetic diversity and population structure of L. coreanus.