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Choi, Jaeyoung,Cheong, Kyeongchae,Jung, Kyongyong,Jeon, Jongbum,Lee, Gir-Won,Kang, Seogchan,Kim, Sangsoo,Lee, Yin-Won,Lee, Yong-Hwan Oxford University Press 2013 Nucleic acids research Vol.41 No.d1
<P>In 2007, Comparative Fungal Genomics Platform (CFGP; http://cfgp.snu.ac.kr/) was publicly open with 65 genomes corresponding to 58 fungal and Oomycete species. The CFGP provided six bioinformatics tools, including a novel tool entitled BLASTMatrix that enables search homologous genes to queries in multiple species simultaneously. CFGP also introduced Favorite, a personalized virtual space for data storage and analysis with these six tools. Since 2007, CFGP has grown to archive 283 genomes corresponding to 152 fungal and Oomycete species as well as 201 genomes that correspond to seven bacteria, 39 plants and 105 animals. In addition, the number of tools in Favorite increased to 27. The Taxonomy Browser of CFGP 2.0 allows users to interactively navigate through a large number of genomes according to their taxonomic positions. The user interface of BLASTMatrix was also improved to facilitate subsequent analyses of retrieved data. A newly developed genome browser, Seoul National University Genome Browser (SNUGB), was integrated into CFGP 2.0 to support graphical presentation of diverse genomic contexts. Based on the standardized genome warehouse of CFGP 2.0, several systematic platforms designed to support studies on selected gene families have been developed. Most of them are connected through Favorite to allow of sharing data across the platforms.</P>
Park, Sook-Young,Choi, Jaeyoung,Lim, Se-Eun,Lee, Gir-Won,Park, Jongsun,Kim, Yang,Kong, Sunghyung,Kim, Se Ryun,Rho, Hee-Sool,Jeon, Junhyun,Chi, Myung-Hwan,Kim, Soonok,Khang, Chang Hyun,Kang, Seogchan,L Public Library of Science 2013 PLoS pathogens Vol.9 No.6
<▼1><P>Because most efforts to understand the molecular mechanisms underpinning fungal pathogenicity have focused on studying the function and role of individual genes, relatively little is known about how transcriptional machineries globally regulate and coordinate the expression of a large group of genes involved in pathogenesis. Using quantitative real-time PCR, we analyzed the expression patterns of 206 transcription factor (TF) genes in the rice blast fungus <I>Magnaporthe oryzae</I> under 32 conditions, including multiple infection-related developmental stages and various abiotic stresses. The resulting data, which are publicly available via an online platform, provided new insights into how these TFs are regulated and potentially work together to control cellular responses to a diverse array of stimuli. High degrees of differential TF expression were observed under the conditions tested. More than 50% of the 206 TF genes were up-regulated during conidiation and/or in conidia. Mutations in ten conidiation-specific TF genes caused defects in conidiation. Expression patterns <I>in planta</I> were similar to those under oxidative stress conditions. Mutants of <I>in planta</I> inducible genes not only exhibited sensitive to oxidative stress but also failed to infect rice. These experimental validations clearly demonstrated the value of TF expression patterns in predicting the function of individual TF genes. The regulatory network of TF genes revealed by this study provides a solid foundation for elucidating how <I>M. oryzae</I> regulates its pathogenesis, development, and stress responses.</P></▼1><▼2><P><B>Author Summary</B></P><P>Rice blast disease, caused by <I>Magnaporthe oryzae</I>, destroys rice crop enough to feed 60 million people every year and has served as a model pathosystem for understanding host-parasite interactions. However, little is known about how <I>M. oryzae</I> globally regulates and coordinates its gene expression at the whole-genome scale. We analyzed the expression patterns of 206 <I>M. oryzae</I> genes encoding transcription factors (TFs) under 32 conditions, including infection-related developmental stages and various abiotic stresses, using quantitative real-time PCR. We focused on identifying the TF genes that are induced during the two most important infection-related morphogenetic changes; conidiation and infectious growth in rice. We identified 57 conidiation-specific TF genes and functionally characterized ten of them. Our data also showed that infectious growth <I>in planta</I> and oxidative stress responses <I>in vitro</I> involve largely overlapping groups of TFs. Comprehensive TF expression data and functional validation provided new insights into the regulatory mechanism underpinning pathogenicity and stress responses in <I>M. oryzae</I>. These data will also serve as a guide in studying the role of individual TF genes and the coordination of their expression in controlling development, pathogenicity, and abiotic stress responses in <I>M. oryzae</I>.</P></▼2>
Ko, Young-Joon,Yu, Yeong Man,Kim, Gyu-Bum,Lee, Gir-Won,Maeng, Pil Jae,Kim, Sangsoo,Floyd, Anna,Heitman, Joseph,Bahn, Yong-Sun American Society for Microbiology 2009 EUKARYOTIC CELL Vol.8 No.8
<B>ABSTRACT</B><P>The ability to sense and adapt to a hostile host environment is a crucial element for virulence of pathogenic fungi, including <I>Cryptococcus neoformans</I>. These cellular responses are evoked by diverse signaling cascades, including the stress-activated HOG pathway. Despite previous analysis of central components of the HOG pathway, its downstream signaling network is poorly characterized in <I>C. neoformans</I>. Here we performed comparative transcriptome analysis with HOG signaling mutants to explore stress-regulated genes and their correlation with the HOG pathway in <I>C. neoformans</I>. In this study, we not only provide important insights into remodeling patterns of global gene expression for counteracting external stresses but also elucidate novel characteristics of the HOG pathway in <I>C. neoformans</I>. First, inhibition of the HOG pathway increases expression of ergosterol biosynthesis genes and cellular ergosterol content, conferring a striking synergistic antifungal activity with amphotericin B and providing an excellent opportunity to develop a novel therapeutic method for treatment of cryptococcosis. Second, a number of cadmium-sensitive genes are differentially regulated by the HOG pathway, and their mutation causes resistance to cadmium. Finally, we have discovered novel stress defense and HOG-dependent genes, which encode a sodium/potassium efflux pump, protein kinase, multidrug transporter system, and elements of the ubiquitin-dependent system.</P>
Kim, Seungill,Park, Minkyu,Yeom, Seon-In,Kim, Yong-Min,Lee, Je Min,Lee, Hyun-Ah,Seo, Eunyoung,Choi, Jaeyoung,Cheong, Kyeongchae,Kim, Ki-Tae,Jung, Kyongyong,Lee, Gir-Won,Oh, Sang-Keun,Bae, Chungyun,Kim Nature Publishing Group, a division of Macmillan P 2014 Nature genetics Vol.46 No.3
Hot pepper (Capsicum annuum), one of the oldest domesticated crops in the Americas, is the most widely grown spice crop in the world. We report whole-genome sequencing and assembly of the hot pepper (Mexican landrace of Capsicum annuum cv. CM334) at 186.6× coverage. We also report resequencing of two cultivated peppers and de novo sequencing of the wild species Capsicum chinense. The genome size of the hot pepper was approximately fourfold larger than that of its close relative tomato, and the genome showed an accumulation of Gypsy and Caulimoviridae family elements. Integrative genomic and transcriptomic analyses suggested that change in gene expression and neofunctionalization of capsaicin synthase have shaped capsaicinoid biosynthesis. We found differential molecular patterns of ripening regulators and ethylene synthesis in hot pepper and tomato. The reference genome will serve as a platform for improving the nutritional and medicinal values of Capsicum species.
Virus Isolation from the First Patient with SARS-CoV-2 in Korea
Wan Beom Park,권낙중,Su Jin Choi,강창경,Pyoeng Gyun Choe,Jin Yong Kim,Jiyoung Yun,Gir-Won Lee,성문우,Nam Joong Kim,서정선,Myoung-don Oh 대한의학회 2020 Journal of Korean medical science Vol.35 No.7
Novel coronavirus (SARS-CoV-2) is found to cause a large outbreak started from Wuhan since December 2019 in China and SARS-CoV-2 infections have been reported with epidemiological linkage to China in 25 countries until now. We isolated SARS-CoV-2 from the oropharyngeal sample obtained from the patient with the first laboratory-confirmed SARS- CoV-2 infection in Korea. Cytopathic effects of SARS-CoV-2 in the Vero cell cultures were confluent 3 days after the first blind passage of the sample. Coronavirus was confirmed with spherical particle having a fringe reminiscent of crown on transmission electron microscopy. Phylogenetic analyses of whole genome sequences showed that it clustered with other SARS- CoV-2 reported from Wuhan.