A5030829735- Mycotoxins in Agriculture and Food
- Fungal Biology and Applications
- Plant Pathogens and Fungal Diseases
- Fungal and yeast genetics research
- Mycorrhizal Fungi and Plant Interactions
- Plant Disease Resistance and Genetics
- Genomics and Phylogenetic Studies
- Cancer-related Molecular Pathways
- Plant Reproductive Biology
- Cancer, Hypoxia, and Metabolism
- Enzyme-mediated dye degradation
- Biofuel production and bioconversion
- Marine and coastal plant biology
- Plant Gene Expression Analysis
- Slime Mold and Myxomycetes Research
- Forest Ecology and Biodiversity Studies
- Microbial Community Ecology and Physiology
- Estrogen and related hormone effects
- Plant and Fungal Interactions Research
- Plant-Microbe Interactions and Immunity
- Ubiquitin and proteasome pathways
- Gastric Cancer Management and Outcomes
- Coral and Marine Ecosystems Studies
- Biocrusts and Microbial Ecology
- Genetic diversity and population structure
Lawrence Berkeley National Laboratory
2020-2024
Joint Genome Institute
2017-2024
United States Department of Energy
2020-2022
Anqing Normal University
2022
Fudan University
2010-2016
Tulane University
2013
Jiangmen Central Hospital
2012
Indiana University Health
2012
Indiana University – Purdue University Indianapolis
2012
Indiana University School of Medicine
2012
Section Flavi encompasses both harmful and beneficial Aspergillus species, such as oryzae, used in food fermentation enzyme production, flavus, spoiler mycotoxin producer. Here, we sequence 19 genomes spanning section compare 31 fungal including 23 species. We reassess their phylogenetic relationships show that the closest relative of A. oryzae is not but minisclerotigenes or aflatoxiformans identify high genome diversity, especially sub-telomeric regions. predict abundant CAZymes (598 per...
Abstract The large size and complexity of most fern genomes have hampered efforts to elucidate fundamental aspects biology land plant evolution through genome-enabled research. Here we present a chromosomal genome assembly associated methylome, transcriptome metabolome analyses for the model species Ceratopteris richardii . reveals history remarkably dynamic including rapid changes in content structure following recent whole-genome duplication approximately 60 million years ago. These...
Abstract As actors of global carbon cycle, Agaricomycetes (Basidiomycota) have developed complex enzymatic machineries that allow them to decompose all plant polymers, including lignin. Among them, saprotrophic Agaricales are characterized by an unparalleled diversity habitats and lifestyles. Comparative analysis 52 genomes (14 sequenced de novo) reveals possess a large hydrolytic oxidative enzymes for lignocellulose decay. Based on the gene families with predicted highest evolutionary...
Abstract Fungal fermentation of food and agricultural by-products holds promise for improving sustainability security. However, the molecular basis fungal waste-to-food upcycling remains poorly understood. Here we use a multi-omics approach to characterize oncom, fermented traditionally produced from soymilk in Java, Indonesia. Metagenomic sequencing samples small-scale producers Western Java indicated that fungus Neurospora intermedia dominates oncom. Further transcriptomic, metabolomic...
AMP-activated protein kinase (AMPK) has been shown to activate p53 in response metabolic stress. However, the underlying mechanisms remain unclear. Here we show that stresses induce AMPK-mediated phosphorylation of human MDMX on Ser342 vitro and cells, leading enhanced association between 14-3-3. This markedly inhibits ubiquitylation significantly stabilizes activates p53. By striking contrast, no MDM2 by AMPK was noted. phosphorylation, MDMX–14-3-3 binding, activation were drastically...
Microbial biosynthetic gene clusters (BGCs) encoding secondary metabolites are thought to impact a plethora of biologically mediated environmental processes, yet their discovery and functional characterization in natural microbiomes remains challenging. Here we describe deep long-read sequencing assembly metagenomes from biological soil crusts, group communities that rich BGCs. Taking advantage the unusually long assemblies produced by this approach, recovered nearly 3,000 BGCs for analysis,...
Lentinula is a broadly distributed group of fungi that contains the cultivated shiitake mushroom, L. edodes . We sequenced 24 genomes representing eight described species and several unnamed lineages from 15 countries on four continents. comprises major clades arose in Oligocene, three Americas one Asia–Australasia. To expand sampling mushrooms, we assembled 60 China were previously published as raw Illumina reads added them to our dataset. sensu lato (s. lat.) may warrant recognition...
Despite various plans to rationalize antibiotic use, resistance in environmental bacteria is increasing due the accumulation of residues environment. This study aimed test ability basidiomycete fungal strains biotransform levofloxacin, a widely-used third-generation broad-spectrum fluoroquinolone, and propose enzyme targets potentially involved this biotransformation. The biotransformation process was performed using strains. Levofloxacin reached 100% after 9 days culture with Porostereum...
Summary The ectomycorrhizal (ECM) symbiosis has independently evolved from diverse types of saprotrophic ancestors. In this study, we seek to identify genomic signatures the transition ECM habit within hyperdiverse Russulaceae. We present comparative analyses architecture and total secreted gene repertoires 18 species across order Russulales, which 13 are newly sequenced, including a representative member Russulaceae, Gloeopeniophorella convolvens . genomes Russulaceae characterized by loss...
Species in the genus Paecilomyces, a member of fungal order Eurotiales, are ubiquitous nature and impact variety human endeavors. Here, biology one common species, Paecilomyces variotii, was explored using genomics functional genetics. Sequencing genome two isolates revealed key gene features this species. A striking feature two-part nature, featuring large stretches DNA with normal GC content separated by AT-rich regions, hallmark many plant-pathogenic genomes. These regions appeared to...
Anaerobic fungi and methanogenic archaea are two classes of microorganisms found in the rumen microbiome that metabolically interact during lignocellulose breakdown. Here, stable synthetic co-cultures anaerobic fungus Caecomyces churrovis methanogen Methanobacterium bryantii (not native to rumen) were formed, demonstrating microbes from different environments can be paired based on metabolic ties. Transcriptional changes induced by co-culture evaluated C. across a variety substrates identify...
Mushroom-forming fungi comprise diverse species that develop complex multicellular structures. In cultivated species, both ecological adaptation and artificial selection have driven genome evolution. However, little is known about the connections among genotype, phenotype in mushroom-forming fungi.This study aimed to (1) uncover population structure demographic history of Lentinula edodes, (2) dissect genetic basis adaptive evolution L. (3) determine if genes related fruiting body...
We assembled the 9.8-Gbp genome of western redcedar (WRC; Thuja plicata), an ecologically and economically important conifer species Cupressaceae. The assembly, derived from a uniquely inbred tree produced through five generations self-fertilization (selfing), was determined to be 86% complete by BUSCO analysis, one most assemblies for conifer. Population genomic analysis revealed WRC genetically depauperate wild plant species, with effective population size approximately 300 no significant...
Wildfires drastically impact the soil environment, altering organic matter, forming pyrolyzed compounds, and markedly reducing diversity of microorganisms. Pyrophilous fungi, especially species from orders Pezizales Agaricales, are fire-responsive fungal colonizers post-fire that have historically been found fruiting on burned thus may encode mechanisms processing these compounds in their genomes. fungi diverse. In this work, we explored sequenced six new genomes pyrophilous isolated after...
Abstract We assembled the 9.8 Gbp genome of western redcedar (WRC, Thuja plicata ), an ecologically and economically important conifer species Cupressaceae. The assembly, derived from a uniquely inbred tree produced through five generations self-fertilization (selfing), was determined to be 86% complete by BUSCO analysis – one most assemblies for conifer. Population genomic revealed WRC genetically depauperate wild plant species, with effective population size approximately 300 no...
Summary Ectomycorrhizal (ECM) fungi are integral to boreal and temperate forest ecosystem functioning nutrient cycling. ECM fungi, however, originate from diverse saprotrophic lineages the impacts of genetic variation across species, especially within a given on function interactions with environment is not well understood. Here, we explore extent intra‐species between four isolates fungus Pisolithus microcarpus , in terms gene regulation, carbon metabolism growth, host, Eucalyptus grandis ....
Forest fires generate a large amount of carbon that remains resident on the site as dead and partially 'pyrolysed' (i.e. burnt) material has long residency times constitutes significant pool in fire-prone ecosystems. In addition, fire-induced hydrophobic soil layers, caused by condensation pyrolysed waxes lipids, increase post-fire erosion can lead to long-term productivity losses. A small set pyrophilous fungi dominate soils are likely be involved with degradation all these compounds, yet...
Summary Transcription factors (TFs) play a central role in regulating gene expression, process fundamental to cellular function. Characterizing transcription factor binding sites (TFBSs) is essential for understanding TF functions and identifying target genes, but many predicted TFBSs lack clear biological significance. We generated an atlas of across ten flowering plants demonstrated that conserved are strongly enriched genomic epigenomic signatures functional regulatory elements. uncovered...
YY1 is a zinc finger transcription factor involved in the regulation of cell growth, development, and differentiation. Although can regulate human papillomavirus-type (HPV) viral oncogenes E6 E7, it remains unknown if plays key role carcinoma progression HPV-infected cells. Here we sought to determine whether upregulated cervical cancer tissues inhibition contributes apoptosis cells, which at least partly p53 dependent. Therefore, be potential therapeutic target for treatment by arsenic...
ABSTRACT Seagrasses comprise the only submerged marine angiosperms, a feat of adaptation from three independent freshwater lineages within Alismatales. These parallel offer unique opportunity to study convergent versus lineage-specific fully lifestyle. Here, we present chromosome-level genome assemblies representative species each seagrass - Posidonia oceanica (Posidoniaceae), Cymodocea nodosa (Cymodoceaceae), and Thalassia testudinum (Hydrocharitaceae) along with an improved assembly for...
Lactic acid bacteria are micro-organisms used for probiotic purposes and form major parts of human mammalian intestinal microbiota, exerting important health-promoting effects on the host. Here, we evaluated Lactobacillus reuteri strain S5 isolated from intestines healthy white feather broilers. grew best after 20 h incubation in MRS medium. production was 1·42 mmol l-1 at 24 h, which well tolerated. Activities T-AOC, GSH-Px T-SOD cell-free fermentation supernatant L. were higher than those...
Vascular development is a regulated process and dependent on the participation differentiation of many cell types including proliferation migration vascular endothelial cells progenitor (EPCs) to mesodermal precursor cells. Thus, reconstitution this in vitro necessitates providing ambient conditions for generating culturing EPCs differentiating them In present study, we developed methods differentiate bone marrow mesenchymal stem (MSC) into Bone MSC from canines human sources were...