A5013910907- Plant Pathogens and Fungal Diseases
- Plant Disease Resistance and Genetics
- Plant-Microbe Interactions and Immunity
- Genomics and Phylogenetic Studies
- Plant and Fungal Interactions Research
- Mycorrhizal Fungi and Plant Interactions
- Silicon Effects in Agriculture
- Parasitic Infections and Diagnostics
- Fungal and yeast genetics research
- Microbial Natural Products and Biosynthesis
- Plant Virus Research Studies
- GABA and Rice Research
- Epigenetics and DNA Methylation
- RNA and protein synthesis mechanisms
- Fungal Biology and Applications
- Chromosomal and Genetic Variations
- Colorectal Cancer Screening and Detection
- Plant Pathogenic Bacteria Studies
- Gut microbiota and health
- Genetic factors in colorectal cancer
- Yeasts and Rust Fungi Studies
- Genetic Associations and Epidemiology
- Genetic Mapping and Diversity in Plants and Animals
- Plant and fungal interactions
- Cancer Genomics and Diagnostics
Chung-Ang University
2024
Korea Research Institute of Bioscience and Biotechnology
2022-2024
Yonsei University
2024
Sage Bionetworks
2023
Seoul National University
2013-2022
National University College
2020
New Generation University College
2020
Chungnam National University
2012
Pennsylvania State University
2012
Transposable elements are major evolutionary forces which can cause new genome structure and species diversification. The role of transposable in the expansion nucleotide-binding leucine-rich-repeat proteins (NLRs), disease-resistance gene families, has been unexplored plants.We report two high-quality de novo genomes (Capsicum baccatum C. chinense) an improved reference (C. annuum) for peppers. Dynamic rearrangements involving translocations among chromosomes 3, 5, 9 were detected...
Abstract Background Plant-associated microbiomes, which are shaped by host and environmental factors, support their hosts providing nutrients attenuating abiotic biotic stresses. Although genetic factors involved in plant growth immunity known to shape compositions of microbial communities, the effects evolution on communities not well understood. Results We show evidence that both speciation domestication seed bacterial fungal community structures. Genome types rice contributed...
Fungal secretome consists of various functional groups proteins, many which participate in nutrient acquisition, self-protection, or manipulation the environment and neighboring organisms. The least characterized component is small secreted proteins (SSPs). Some SSPs have been reported to function as effectors, but most remain be characterized. composition major components, such carbohydrate-active enzymes, proteases, lipases, oxidoreductases, appear reflect lifestyle ecological niche...
Abstract Pathogens utilize multiple types of effectors to modulate plant immunity. Although many apoplastic and cytoplasmic have been reported, nuclear not well characterized in fungal pathogens. Here, we characterize two the rice blast pathogen Magnaporthe oryzae . Both are secreted via biotrophic interfacial complex, translocated into nuclei initially penetrated surrounding cells, reprogram expression immunity-associated genes by binding on effector elements rice. Their transgenic causes...
Abstract Vertical transmission of microbes is crucial for the persistence host-associated microbial communities. Although vertical seed has been reported from diverse plants, ecological mechanisms and dynamics communities parent to progeny remain scarce. Here we reveal veiled mechanism governing bacterial fungal in rice across two consecutive seasons. We identify 29 34 members transmitted generations. Abundance-based regression models allow classify colonization types microbes. find that...
Plant cell wall-degrading enzymes (PCWDEs) play significant roles throughout the fungal life including acquisition of nutrients and decomposition plant walls. In addition, many PCWDEs are also utilized by biofuel pulp industries. order to develop a comparative genomics platform focused in provide resource for evolutionary studies, Fungal PCWDE Database (FPDB) is constructed ( http://pcwde.riceblast.snu.ac.kr/ ). archive PCWDEs, 22 sequence profiles were searched on 328 genomes fungi,...
Every year, 11% of infants are born preterm with significant health consequences, the vaginal microbiome a risk factor for birth. We crowdsource models to predict (1) birth (PTB; <37 weeks) or (2) early (ePTB; <32 from 9 studies representing 3,578 samples 1,268 pregnant individuals, aggregated public raw data via phylogenetic harmonization. The predictive validated on two independent unpublished datasets 331 148 individuals. top-performing (among and 121 submissions 318 teams) achieve area...
The onion (Allium cepa L.) is one of the most widely cultivated and consumed vegetable crops in world. Although a considerable amount transcriptome data has been deposited into public databases, sequences protein-coding genes are not accurate enough to be used, owing non-coding intermixed with coding sequences. We generated high-quality, annotated from de novo sequence assembly intensive structural annotation using integrated gene pipeline (ISGAP), which identified 54,165 among 165,179...
Abstract Background Phenome-wide association studies (PheWASs) have been conducted on Asian populations, including Koreans, but many were based chip or exome genotyping data. Such limitations regarding whole genome–wide analysis, making it crucial to genome-to-phenome information with the largest possible genome and matched phenome data conduct further population-genome develop health care services population genomics. Results Here, we present 4,157 sequences (Korea4K) coupled 107 check-up...
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 queries in multiple species simultaneously. also introduced Favorite, personalized virtual space for data storage analysis these tools. Since has grown archive 283 152 as well 201 correspond seven bacteria, 39...
RNA interference (RNAi) is involved in genome defense as well diverse cellular, developmental, and physiological processes. Key components of RNAi are Argonaute, Dicer, RNA-dependent polymerase (RdRP), which have been functionally characterized mainly model organisms. The key believed to exist throughout eukaryotes; however, there no systematic platform for archiving dissecting these important gene families. In addition, few fungi studied date, limiting our understanding fungi. Here we...
Alternative splicing (AS) contributes to diversifying and regulating cellular responses environmental conditions developmental cues by differentially producing multiple mRNA protein isoforms from a single gene. Previous studies on AS in pathogenic fungi focused profiling under limited number of conditions. We analysed profiles the rice blast fungus Magnaporthe oryzae, global threat production, using high-quality transcriptome data representing its vegetative growth (mycelia) host infection...
Abstract Hot pepper ( Capsicum annuum ) is one of the most consumed vegetable crops in world and useful to human as it has many nutritional medicinal values. Genomic resources are publically available since genomes have been completed massive data such transcriptomes deposited. Nevertheless, global transcriptome profiling needed identify molecular mechanisms related agronomic traits pepper, but limited analyses published. Here, we report comprehensive analysis during fruit ripening pathogen...
The rice blast (fungal pathogen: Magnaporthe oryzae and host: Oryza sativa) is one of the most important model pathosystems for understanding plant-microbe interactions. Although both genome sequences were published as first cases pathogen host, only a few in planta transcriptome data during infection are available. Due to technical difficulties, previously reported fungal not highly qualified comprehensively profile expression genes infection. Here, we report high-quality transcriptomes M....
Magnaporthe oryzae infects rice, wheat, and many grass species in the Poaceae family by secreting protein effectors. Here, we analyzed distribution, sequence variation, genomic context of effector candidate (EFC) genes 31 isolates that represent five pathotypes M. oryzae, three grisea, a sister one strain each for eight Magnaporthaceae to investigate how host range expansion has likely affected evolution We used EFC 70-15, whose genome served as reference comparative genomics analyses,...
Abstract Background Plant pathogenic isolates of Rhizoctonia solani anastomosis group 1-intraspecific IA (AG1-IA) infect a wide range crops causing diseases such as rice sheath blight (ShB). ShB has become serious disease in production worldwide. Additional genome sequences the rice-infecting R. from different geographical regions will facilitate identification important pathogenicity-related genes fungus. Results Rice-infecting B2 (USA), ADB (India), WGL and YN-7 (China) were selected for...
Abstract Globally, every year about 11% of infants are born preterm, defined as a birth prior to 37 weeks gestation, with significant and lingering health consequences. Multiple studies have related the vaginal microbiome preterm birth. We present crowdsourcing approach predict: (a) or (b) early from 9 publicly available representing 3,578 samples 1,268 pregnant individuals, aggregated raw sequences via an open-source tool, MaLiAmPi. validated crowdsourced models on novel datasets 331 148...
A wave of new technologies has created opportunities for the cost-effective generation high-throughput profiles biological systems, foreshadowing a "data-driven science" era. The large variety data available from research is also rich resource that can be used innovative endeavors. However, we are facing considerable challenges in big deposition, integration, and translation due to complexity its production at unprecedented exponential rates. To address these problems, 2020, Korean...
Abstract During the last decade, generation and accumulation of petabase-scale high-throughput sequencing data have resulted in great challenges, including access to human data, as well transfer, storage, sharing enormous amounts data. To promote data-driven biological research, Korean government announced that all generated from government-funded research projects should be deposited at Korea BioData Station (K-BDS), which consists multiple databases for individual types. Here, we introduce...
Summary Whole‐genome annotation error that omits essential protein‐coding genes hinders further research. We developed Target Gene Family Finder ( TGFam‐Finder ), an alternative tool for the structural of containing target domain(s) interest in plant genomes. took considerably reduced run‐time and improved accuracy compared to conventional tools. Large‐scale re‐annotation 50 genomes identified average 150, 166 86 additional far‐red‐impaired response 1, nucleotide‐binding leucine‐rich‐repeat,...
Long non-coding RNAs (lncRNAs) play essential roles in developmental processes and disease development at the transcriptional post-transcriptional levels across diverse taxa. However, only few studies have profiled fungal lncRNAs a genome-wide manner during host infection.Infection-associated were identified using lncRNA profiling over six stages of infection (e.g., vegetative growth, pre-penetration, biotrophic, necrotrophic stages) model pathogenic fungus, Magnaporthe oryzae. We 2,601...
Abstract Lichen-forming fungi are mutualistic symbionts of green algae or cyanobacteria. We report the comparative analysis six genomes lichen-forming in classes Eurotiomycetes and Lecanoromycetes to identify genomic information related their symbiotic lifestyle. The exhibited genome reduction via loss dispensable genes encoding plant-cell-wall-degrading enzymes, sugar transporters, transcription factors. these reflects biology lichens, such as absence pectin algal cell wall obtaining...
Acetylation of histone H3 lysine 56 (H3K56) by the fungal-specific acetyltransferase Rtt109 plays important roles in maintaining genome integrity and surviving DNA damage. Here, we investigated implications Rtt109-mediated response to damage on development pathogenesis rice blast fungus Magnaporthe oryzae (anamorph: Pyricularia oryzae). The ortholog M. (MoRtt109) was found via sequence homology its functionality confirmed phenotypic complementation Saccharomyces cerevisiae deletion strain....
Colletotrichum has a broad host range and causes major yield losses of crops. The fungus gloeosporioides is associated with anthracnose on Chinese fir. In this study, we present high-quality draft genome sequence C. sensu stricto SMCG1#C, providing reference genomic data for further research fir other hosts.
The soil environment determines plants’ health and performance during their life cycle. Therefore, ecological understanding on variations in environments, including physical, chemical, biological properties, is crucial for managing agricultural fields. Here, we present a comprehensive extensive blueprint of the bacterial, archaeal, fungal communities rice paddy soils with differing types chemical properties. We discovered that natural nutrients are important factors shaping microbial...