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Genome wide analysis of rice blast pathogen, Magnaporthe oryzae, in Korea
Yoonhee KIM,Hyejeong KIM,Jinsoo KIM,Miyeon JEONG,Soyoung PARK,Suyoung KIM,Jongsun Park,Soonok KIM,Yong-Hwan LEE,Seong Sook HAN,Jae Hwan ROH,Woobong CHOI 한국작물학회 2007 한국작물학회 학술발표대회 논문집 Vol.2007 No.11
Magnaporthe oryzae is a causal pathogen of the rice blast, the most destructive disease of rice worldwide. This ascomycete fungus has been intensively studied as a model organism in plant-pathogen interactions. Recently, the genome sequence of M. oryzae 70-15 was published by International Rice Blast Consortium. This led us to investigate comparative and functional analysis of this pathogen at genome-wide level. As a first step, sequencing project of M. oryzae Korean strain KJ201 was launched to face practical interests on diversity of plant pathogens. We constructed a fosmid library with a copy number controllable pCC1 vector. Over 13,000 end reads from 6637 fosmid clones were generated and anchored on genome sequence of the strain 70-15. Currently, 9,793 end reads, in which 2.684, clones with both ends and 1,757 clones with on end matched, are aligned to the sequence of strain 70-15. In the next step, shotgun sequencing of fosmid clones was conducted for fine scale comparative analysis of chromosome 7 that is well defined in genome sequencing of 70-15. Totally 119 fosmid clones were pooled in region and analyzed. For reasonable intra-species comparison in genome of M. oryzae, two strains, KJ201 and Guy11, were chosen for whole genome shotgun sequencing analysis with GS454 FLX system. About 8X genome coverage sequences were obtained for each strain and being merged for comparative analysis. Genome information of other strains is being also available from China and Japanese research groups and could be joined together for extended comparative analysis and the results give more detail in genome diversity in species level.
Kim, Soonok,Ahn, Il‐,Pyung,Rho, Hee‐,Sool,Lee, Yong‐,Hwan Blackwell Science Ltd 2005 Molecular microbiology Vol.57 No.5
<P><B>Summary</B></P><P>Fungal hydrophobins are implicated in cell morphogenesis and pathogenicity in several plant pathogenic fungi including the rice blast fungus <I>Magnaporthe grisea</I>. A cDNA clone encoding a hydrophobin (magnaporin, <I>MHP1</I>) was isolated from a cDNA library constructed from rice leaves infected by <I>M. grisea</I>. The <I>MHP1</I> codes for a typical fungal hydrophobin of 102 amino acids containing eight cysteine residues spaced in a conserved pattern. Hydropathy analysis of amino acids revealed that MHP1 belongs to the class II group of hydrophobins. The amino acid sequence of MHP1 exhibited about 20% similarity to MPG1, an <I>M. grisea</I> class I hydrophobin. Expression of <I>MHP1</I> was highly induced during plant colonization and conidiation, but could hardly be detected during mycelial growth. Transformants in which <I>MHP1</I> was inactivated by targeted gene replacement showed a detergent wettable phenotype, but were not altered in wettability with water. <I>mhp1</I> mutants also exhibited pleiotropic effects on fungal morphogenesis, including reduction in conidiation, conidial germination, appressorium development and infectious growth in host cells. Furthermore, conidia of <I>mhp1</I> mutants were defective in their cellular organelles and rapidly lose viability. As a result, <I>mhp1</I> mutants exhibited a reduced ability to infect and colonize a susceptible rice cultivar. These phenotypes were recovered by re‐introduction of an intact copy of <I>MHP1</I>. Taken together, these results indicate that <I>MHP1</I> has essential roles in surface hydrophobicity and infection‐related fungal development, and is required for pathogenicity of <I>M. grisea</I>.</P>
Kim, Soonok,Hu, Jinnan,Oh, Yeonyee,Park, Jongsun,Choi, Jinhee,Lee, Yong-Hwan,Dean, Ralph A.,Mitchell, Thomas K. Public Library of Science 2010 PLoS pathogens Vol.6 No.5
<▼1><P>Significant progress has been made in defining the central signaling networks in many organisms, but collectively we know little about the downstream targets of these networks and the genes they regulate. To reconstruct the regulatory circuit of calcineurin signal transduction via <I>MoCRZ1</I>, a <I>Magnaporthe oryzae</I> C2H2 transcription factor activated by calcineurin dephosphorylation, we used a combined approach of chromatin immunoprecipitation - chip (ChIP-chip), coupled with microarray expression studies. One hundred forty genes were identified as being both a direct target of MoCRZ1 and having expression concurrently differentially regulated in a calcium/calcineurin/MoCRZ1 dependent manner. Highly represented were genes involved in calcium signaling, small molecule transport, ion homeostasis, cell wall synthesis/maintenance, and fungal virulence. Of particular note, genes involved in vesicle mediated secretion necessary for establishing host associations, were also found. <I>MoCRZ1</I> itself was a target, suggesting a previously unreported autoregulation control point. The data also implicated a previously unreported feedback regulation mechanism of calcineurin activity. We propose that calcium/calcineurin regulated signal transduction circuits controlling development and pathogenicity manifest through multiple layers of regulation. We present results from the ChIP-chip and expression analysis along with a refined model of calcium/calcineurin signaling in this important plant pathogen.</P></▼1><▼2><P><B>Author Summary</B></P><P>All organisms have the innate ability to perceive their environment and respond to it, largely through controlling gene expression. Tailored specificity of a response is primarily achieved through signal cascades involving unique receptors, downstream transcription factors (proteins that bind to DNA to regulate gene expression), and the genes these transcription factors regulate. For fungal plant pathogens, signal transduction cascades are involved in perception of hosts, transgression of physical barriers, suppression or elicitation of host defenses, <I>in vivo</I> nutrient acquisition, and completion of their life cycle. We know that the Ca<SUP>2+</SUP>/calcineurin signaling pathway is a central conduit regulating these aspects of the life cycle for fungal pathogens of plants and animals. In this study, we used advanced ChIP-chip and microarray gene expression technologies to identify the genes that the Ca<SUP>2+</SUP>/calcineurin responsive transcription factor MoCRZ1 directly binds to and regulates the expression of. Our findings show conservations and divergence in this pathway within the fungal kingdom. It also identifies points of control in the pathway that were previously unidentified. Most importantly, this study implicates this pathway in the establishment of host associations and virulence for the causal agent of rice blast disease, <I>Magnaporthe oryzae</I>, the most important disease of rice worldwide.</P></▼2>
( Soonok Kim ),( Yun Sung Cho ),( Jong Bhak ),( Stephen J. O`brian ),( Joo-hong Yeo ) 생화학분자생물학회(구 한국생화학분자생물학회) 2017 BMB Reports Vol.50 No.1
Recent advances in genome sequencing technologies have enabled humans to generate and investigate the genomes of wild species. This includes the big cat family, such as tigers, lions, and leopards. Adding the first high quality leopard genome, we have performed an in-depth comparative analysis to identify the genomic signatures in the evolution of felid to become the top predators on land. Our study focused on how the carnivore genomes, as compared to the omnivore or herbivore genomes, shared evolutionary adaptations in genes associated with nutrient metabolism, muscle strength, agility, and other traits responsible for hunting and meat digestion. We found genetic evidence that genomes represent what animals eat through modifying genes. Highly conserved genetically relevant regions were discovered in genomes at the family level. Also, the Felidae family genomes exhibited low levels of genetic diversity associated with decreased population sizes, presumably because of their strict diet, suggesting their vulnerability and critical conservation status. Our findings can be used for human health enhancement, since we share the same genes as cats with some variation. This is an example how wildlife genomes can be a critical resource for human evolution, providing key genetic marker information for disease treatment. [BMB Reports 2017; 50(1): 3-4]
김순옥(Kim, Soonok),윤규철(Yoon, Kyuchul) 한국음성학회 2015 말소리와 음성과학 Vol.7 No.2
The purpose of this paper is to extract the vowel formants of the ten adult male speakers in their twenties and thirties from the Korean Corpus of Spontaneous Speech [4], also known as the Seoul corpus, and to analyze them by comparing to earlier works on the Buckeye Corpus of Conversational Speech [1] in terms of the various linguistic factors that are expected to affect the formant distribution. The vowels extracted from the Korean corpus were also compared to those of the read Korean. The results showed that the distribution of the vowel formants from the Korean corpus was very different from that of read Korean speech. The comparison with English corpus and read English speech showed similar patterns. The factors affecting the Korean vowel formants were the interviewer sex, the location of the target vowel or the syllable containing it with respect to the phrasal word or utterance and the speech rate of the surrounding words.