A5064531963- Genomics and Phylogenetic Studies
- Plant Pathogens and Fungal Diseases
- Plant and Fungal Species Descriptions
- Genetic diversity and population structure
- Plant and animal studies
- Insect-Plant Interactions and Control
- Plant Virus Research Studies
- Insect and Arachnid Ecology and Behavior
- Insect symbiosis and bacterial influences
- Mycorrhizal Fungi and Plant Interactions
- Plant-Microbe Interactions and Immunity
- Bryophyte Studies and Records
- Plant Taxonomy and Phylogenetics
- Fungal and yeast genetics research
- Plant Disease Resistance and Genetics
- Fungal Biology and Applications
- Ecology and Conservation Studies
- Plant Diversity and Evolution
- Microbial Natural Products and Biosynthesis
- Phytoplasmas and Hemiptera pathogens
- Yeasts and Rust Fungi Studies
- Plant biochemistry and biosynthesis
- Agriculture, Soil, Plant Science
- Cocoa and Sweet Potato Agronomy
- Phytochemistry and Biological Activities
Kyungpook National University
2025
Pusan National University
2025
Daejeon University
2023-2024
Sejong University
2024
Gachon University
2021-2023
Sungkyunkwan University
2013-2019
Infosys (India)
2019
SK Group (South Korea)
2018
Keimyung University
2011-2014
Genome Research Foundation
2012-2014
Fusarium species are among the most important phytopathogenic and toxigenic fungi. To understand molecular underpinnings of pathogenicity in genus Fusarium, we compared genomes three phenotypically diverse species: graminearum, verticillioides oxysporum f. sp. lycopersici. Our analysis revealed lineage-specific (LS) genomic regions F. that include four entire chromosomes account for more than one-quarter genome. LS rich transposons genes with distinct evolutionary profiles but related to...
ABSTRACT Because less than one-third of clinically relevant fusaria can be accurately identified to species level using phenotypic data (i.e., morphological recognition), we constructed a three-locus DNA sequence database facilitate molecular identification the 69 Fusarium associated with human or animal mycoses encountered in clinical microbiology laboratories. The comprises partial sequences from three nuclear genes: translation elongation factor 1α ( EF-1α ), largest subunit RNA...
Comparative genomic analysis of “dry rot” fungus shows both convergent evolution and divergence among fungal decomposers.
The vascular wilt fungi Verticillium dahliae and V. albo-atrum infect over 200 plant species, causing billions of dollars in annual crop losses. characteristic symptoms are a result colonization proliferation the pathogens xylem vessels, which undergo fluctuations osmolarity. To gain insights into mechanisms that confer organisms' pathogenicity enable them to proliferate unique ecological niche system, we sequenced genomes compared each other, genome Fusarium oxysporum, another fungal...
• Parasitism and saprotrophic wood decay are two fungal strategies fundamental for succession nutrient cycling in forest ecosystems. An opportunity to assess the trade-off between these is provided by pathogen decayer Heterobasidion annosum sensu lato. We report annotated genome sequence transcript profiling, as well quantitative trait loci mapping, of one member species complex: H. irregulare. Quantitative critical pathogenicity, rich transposable elements, orphan secreted genes, were...
The appropriate development of conidia and appressoria is critical in the disease cycle many fungal pathogens, including Magnaporthe oryzae. A total eight genes (MoHOX1 to MoHOX8) encoding putative homeobox transcription factors (TFs) were identified from M. oryzae genome. Knockout mutants for each MoHOX gene obtained via homology-dependent replacement. Two mutants, ΔMohox3 ΔMohox5, exhibited no difference wild-type growth, conidiation, conidium size, conidial germination, appressorium...
Abstract Background Fungi secrete various proteins that have diverse functions. Prediction of secretory using only one program is unsatisfactory. To enhance prediction accuracy, we constructed Fungal Secretome Database (FSD). Description A three-layer hierarchical identification rule based on nine programs was used to identify putative in 158 fungal/oomycete genomes (208,883 proteins, 15.21% the total proteome). The presence effectors containing known host targeting signals such as RXLX...
Abstract Summary: Genomes of more than 60 fungal species have been sequenced to date, yet there has no systematic approach analyze transcription factors (TFs) kingdom widely. We developed a standardized pipeline for annotating TFs in genomes. Resulting data archived new database termed the Fungal Transcription Factor Database (FTFD). In FTFD, 31 832 putative TFs, identified from 62 and 3 Oomycete species, were classified into 61 families phylogenetically analyzed. The FTFD will serve as...
Cytochrome P450 enzymes play critical roles in fungal biology and ecology. To support studies on the evolution of cytochrome fungi based rapidly accumulating genome sequences from diverse species, an efficient bioinformatics platform specialized for this super family proteins is highly desirable.The Fungal Database (FCPD) archives genes encoding P450s genomes 66 4 oomycete species (4,538 total) supports analyses their sequences, chromosomal distribution pattern, evolutionary histories...
Cytochrome P450 proteins (CYPs) play diverse and pivotal roles in fungal metabolism adaptation to specific ecological niches. Fungal genomes encode extremely variable "CYPomes" ranging from one more than 300 CYPs. Despite the rapid growth of sequenced oomycete resulting influx predicted CYPs, vast majority CYPs remain functionally uncharacterized. To facilitate curation functional evolutionary studies we previously developed Database (FCPD), which included 70 species. Here present a new...
Bemisia tabaci (Hemiptera: Aleyrodidae) is one of the most important insect pests in world. In present study, taxonomic status B. and number species composing complex were determined based on 1059 COI sequences 509 153 hemipteran species. The genetic divergence within was conspicuously higher (on average, 11.1%) than interspecific respective genera 6.5%). This result indicates that composed multiple may belong to different or subfamilies. A phylogenetic tree constructed 212 without...
Insertional mutagenesis of Magnaporthe oryzae led to the identification MCK1, a pathogenicity gene predicted encode mitogen-activated protein kinase (MAPKKK) homologous BCK1 in Saccharomyces cerevisiae. Targeted disruption MCK1 resulted fungus undergoing autolysis and showing hypersensitivity cell-wall-degrading enzyme. The mck1 produced significantly reduced numbers conidia developed appressoria slightly retarded manner compared with wild type. Appressorium mutant was unable penetrate into...
Abstract 2’-O-methylation (2OM) is the most common post-transcriptional modification of RNA. It plays a crucial role in RNA splicing, stability and innate immunity. Despite advances high-throughput detection, chemical 2OM makes it difficult to detect map messenger Therefore, bioinformatics tools have been developed using machine learning (ML) algorithms identify sites. These made significant progress, but their performances remain unsatisfactory need further improvement. In this study, we...
Abstract Background Thoroughbred horses are the most expensive domestic animals, and their running ability knowledge about muscle-related diseases important in animal genetics. While horse reference genome is available, there has been no large-scale functional annotation of using expressed genes derived from transcriptomes. Results We present a analysis whole transcriptome data. sequenced mRNA blood muscle tissues six thoroughbred before after exercise. By comparing current annotations, we...
Since the completion of Saccharomyces cerevisiae genome sequencing project in 1996, genomes over 80 fungal species have been sequenced or are currently being sequenced. Resulting data provide opportunities for studying and comparing biology evolution at level. To support such studies, Comparative Fungal Genomics Platform (CFGP; http://cfgp.snu.ac.kr), a web-based multifunctional informatics workbench, was developed. The CFGP comprises three layers, including basal layer, middleware user...
Abstract Background Simple sequence repeats (SSRs) have been successfully used for various genetic and evolutionary studies in eukaryotic systems. The model organism Neurospora crassa is an excellent system to study evolution biological function of SSRs. Results We identified characterized 2749 SSRs 963 SSR types the genome N. . distribution tri-nucleotide (nt) SSRs, most common , was significantly biased exons. further 19 abundant (AST), which account 71% total genome, using a Poisson...
Summary A grobacterium t umefaciens‐ m ediated ransformation (ATMT) has become a prevalent tool for functional genomics of fungi, but our understanding T‐DNA integration into the fungal genome remains limited relative to that in plants. Using model plant‐pathogenic fungus, Magnaporthe oryzae , here we report most comprehensive analysis events fungi and development an informatics infrastructure, termed T ‐DNA nalysis p latform (TAP). We identified total 1110 ‐DNA‐ agged l ocations (TTLs)...
The fungal genus Fusarium includes many plant and/or animal pathogenic species and produces diverse toxins. Although accurate identification is critical for managing such threats, it difficult to identify morphologically. Fortunately, extensive molecular phylogenetic studies, founded on well-preserved culture collections, have established a robust foundation classification. Genomes of four been published with more being currently sequenced. Cyber infrastructure (CiF;...
Because most efforts to understand the molecular mechanisms underpinning fungal pathogenicity have focused on studying function and role of individual genes, relatively little is known about how transcriptional machineries globally regulate coordinate expression a large group genes involved in pathogenesis. Using quantitative real-time PCR, we analyzed patterns 206 transcription factor (TF) rice blast fungus Magnaporthe oryzae under 32 conditions, including multiple infection-related...
Microsatellite instability (MSI) is a critical mechanism that drives genetic aberrations in cancer. To identify the entire MS mutation, we performed first comprehensive genome- and transcriptome-wide analyses of mutations associated with MSI Korean gastric cancer cell lines primary tissues. We identified 18,377 five or more repeat nucleotides coding sequences untranslated regions genes, discovered 139 individual genes whose expression was down-regulated association UTR mutation. In addition,...