Robin A. Ohm
A5002783785- Fungal Biology and Applications
- Mycorrhizal Fungi and Plant Interactions
- Plant Pathogens and Fungal Diseases
- Fungal and yeast genetics research
- Plant-Microbe Interactions and Immunity
- Enzyme-mediated dye degradation
- Entomopathogenic Microorganisms in Pest Control
- Plant tissue culture and regeneration
- Insect and Arachnid Ecology and Behavior
- Fermentation and Sensory Analysis
- Plant Disease Resistance and Genetics
- Pediatric health and respiratory diseases
- Interstitial Lung Diseases and Idiopathic Pulmonary Fibrosis
- Yeasts and Rust Fungi Studies
- Genomics and Phylogenetic Studies
- Microbial Community Ecology and Physiology
- Biofuel production and bioconversion
- Forest Insect Ecology and Management
- Plant Gene Expression Analysis
- Mycotoxins in Agriculture and Food
- Forest Ecology and Biodiversity Studies
- CRISPR and Genetic Engineering
- Insect and Pesticide Research
- Protist diversity and phylogeny
- Polysaccharides and Plant Cell Walls
Utrecht University
2015-2024
TiFN
2020-2023
Lawrence Berkeley National Laboratory
2011-2023
Joint Genome Institute
2012-2022
United States Department of Energy
2012-2018
KBase
2013-2015
Cancer Genomics Centre
2009-2014
Wood is a major pool of organic carbon that highly resistant to decay, owing largely the presence lignin. The only organisms capable substantial lignin decay are white rot fungi in Agaricomycetes, which also contains non-lignin-degrading brown and ectomycorrhizal species. Comparative analyses 31 fungal genomes (12 generated for this study) suggest lignin-degrading peroxidases expanded lineage leading ancestor reconstructed as species, then contracted parallel lineages mycorrhizal Molecular...
MycoCosm is a fungal genomics portal (http://jgi.doe.gov/fungi), developed by the US Department of Energy Joint Genome Institute to support integration, analysis and dissemination genome sequences other 'omics' data providing interactive web-based tools. also promotes facilitates user community participation through nomination new species fungi for sequencing, annotation resulting data. By efficiently filling gaps in Fungal Tree Life, will help address important problems associated with...
Francis Martin and colleagues report genome sequences for 18 species of mycorrhizal fungi a phylogenomic analysis including 32 other fungal genomes. The study identifies cell wall-degradation genes lost in all true ectomycorrhizal and, using gene expression data, finds candidate the establishment symbiosis. To elucidate genetic bases lifestyle evolution, we sequenced new genomes, 13 (ECM), orchid (ORM) ericoid (ERM) species, five saprotrophs, which analyzed along with Ectomycorrhizal have...
The class Dothideomycetes is one of the largest groups fungi with a high level ecological diversity including many plant pathogens infecting broad range hosts. Here, we compare genome features 18 members this class, 6 necrotrophs, 9 (hemi)biotrophs and 3 saprotrophs, to analyze structure, evolution, diverse strategies pathogenesis. most likely evolved from common ancestor more than 280 million years ago. sequences differ dramatically in size due variation repetitive content, but show much...
The Department of Energy (DOE) Joint Genome Institute (JGI) is a national user facility with massive-scale DNA sequencing and analysis capabilities dedicated to advancing genomics for bioenergy environmental applications. Beyond generating tens trillions bases annually, the develops maintains data management systems specialized analytical manage interpret complex genomic sets, enable an expanding community users around world analyze these in different contexts over web. JGI Portal...
Much remains to be learned about the biology of mushrooms, which are an important source food as well secondary metabolites and enzymes biotechnological importance. Ohm et al. report sequence genetically tractable species Schizophyllum commune identify genes involved in formation fruiting bodies degradation lignocellulose. mushroom-forming fungi, food, industrial enzymes. The wood-degrading fungus is both a model for studying mushroom development likely capable efficient lignocellulosic...
Agaricus bisporus is the model fungus for adaptation, persistence, and growth in humic-rich leaf-litter environment. Aside from its ecological role, A. has been an important component of human diet over 200 y worldwide cultivation "button mushroom" forms a multibillion dollar industry. We present two genomes, their gene repertoires transcript profiles on compost during mushroom formation. The genomes encode full repertoire polysaccharide-degrading enzymes similar to that wood-decayers....
Mycorrhizal fungi are mutualists that play crucial roles in nutrient acquisition terrestrial ecosystems. symbioses arose repeatedly across multiple lineages of Mucoromycotina, Ascomycota, and Basidiomycota. Considerable variation exists the capacity mycorrhizal to acquire carbon from soil organic matter. Here, we present a combined analysis 135 fungal genomes 73 saprotrophic, endophytic pathogenic species, 62 including 29 new genomes. This study samples ecologically dominant guilds for which...
Significance The highly diverse Ascomycete yeasts have enormous biotechnological potential. Collectively, these convert a broad range of substrates into useful compounds, such as ethanol, lipids, and vitamins, can grow in extremes temperature, salinity, pH. We compared 29 yeast genomes with the goal correlating genetics to traits. In one rare species, we discovered genetic code that translates CUG codons alanine rather than canonical leucine. Genome comparison enabled correlation genes...
Aureobasidium pullulans is a black-yeast-like fungus used for production of the polysaccharide pullulan and antimycotic aureobasidin A, as biocontrol agent in agriculture. It can cause opportunistic human infections, it inhabits various extreme environments. To promote understanding these traits, we performed de-novo genome sequencing four varieties A. pullulans.
We sequenced and compared the genomes of Dothideomycete fungal plant pathogens Cladosporium fulvum (Cfu) (syn. Passalora fulva) Dothistroma septosporum (Dse) that are closely related phylogenetically, but have different lifestyles hosts. Although both fungi grow extracellularly in close contact with host mesophyll cells, Cfu is a biotroph infecting tomato, while Dse hemibiotroph pine. The these similar set genes (70% gene content homologs), differ significantly size (Cfu >61.1-Mb; 31.2-Mb),...
Abstract Mushroom-forming fungi (Agaricomycetes) have the greatest morphological diversity and complexity of any group fungi. They radiated into most niches fulfil diverse roles in ecosystem, including wood decomposers, pathogens or mycorrhizal mutualists. Despite importance mushroom-forming fungi, large-scale patterns their evolutionary history are poorly known, part due to lack a comprehensive dated molecular phylogeny. Here, using multigene genome-based data, we assemble 5,284-species...
The genomes of five Cochliobolus heterostrophus strains, two sativus three additional species (Cochliobolus victoriae, carbonum, miyabeanus), and closely related Setosphaeria turcica were sequenced at the Joint Genome Institute (JGI). datasets used to identify SNPs between strains species, unique genomic regions, core secondary metabolism genes, small secreted protein (SSP) candidate effector encoding genes with a view towards pinpointing structural elements gene content associated...
Evolution of lignocellulose decomposition was one the most ecologically important innovations in fungi. White-rot fungi Agaricomycetes (mushrooms and relatives) are effective microorganisms degrading both cellulose lignin components woody plant cell walls (PCW). However, precise evolutionary origins poorly understood, largely because certain early-diverging clades its sister group, Dacrymycetes, have yet to be sampled, or been undersampled, comparative genomic studies. Here, we present new...
Summary Some soil fungi in the Leotiomycetes form ericoid mycorrhizal ( ERM ) symbioses with Ericaceae. In harsh habitats which they occur, plant survival relies on nutrient mobilization from organic matter SOM by their fungal partners. The characterization of genetic machinery underpinning both symbiotic lifestyle and degradation is needed to understand symbiosis functioning evolution, its impact carbon (C) turnover. We sequenced genomes Meliniomyces bicolor , M. variabilis Oidiodendron...
Dothideomycetes is the largest class of kingdom Fungi and comprises an incredible diversity lifestyles, many which have evolved multiple times. Plant pathogens represent a major ecological niche they are known to infect most food crops feedstocks for biomass biofuel production. Studying ecology evolution has significant implications our fundamental understanding fungal evolution, their adaptation stress host specificity, practical with regard effects climate change on food, feed, livestock...
As decomposers, fungi are key players in recycling plant material global carbon cycles. We hypothesized that genomes of early diverging may have inherited pectinases from an ancestral species had been able to extract nutrients pectin-containing land plants and their algal allies (Streptophytes). aimed infer, based on pectinase gene expansions the organismal phylogeny, geological timing plant–fungus association. analyzed 40 fungal genomes, three which, including Gonapodya prolifera , were...
Dark septate endophytes (DSE) are a form-group of root endophytic fungi with elusive functions. Here, the genomes two common DSE semiarid areas, Cadophora sp. and Periconia macrospinosa were sequenced analyzed another 32 ascomycetes different lifestyles. (Helotiales) P. (Pleosporales) have 70.46 Mb 54.99 22,766 18,750 gene models, respectively. The majority DSE-specific protein clusters lack functional annotation no similarity to characterized proteins, implying that they evolved unique...
Abstract The most frequently encountered symbiont on tree roots is the ascomycete Cenococcum geophilum, only mycorrhizal species within largest fungal class Dothideomycetes, a known for devastating plant pathogens. Here we show that symbiotic genomic idiosyncrasies of ectomycorrhizal basidiomycetes are also present in C. geophilum with symbiosis-induced, taxon-specific genes unknown function and reduced numbers cell wall-degrading enzymes. still holds significant set categories to be...
Endosymbiosis of bacteria by eukaryotes is a defining feature cellular evolution. In addition to well-known bacterial origins for mitochondria and chloroplasts, multiple endosymbiosis are known within the cells diverse animals, plants fungi. Early-diverging lineages terrestrial fungi harbor endosymbiotic belonging Burkholderiaceae. We sequenced metagenome soil-inhabiting fungus Mortierella elongata assembled complete circular chromosome its endosymbiont, Mycoavidus cysteinexigens, which we...
Adaptive manipulation of animal behavior by parasites functions to increase parasite transmission through changes in host behavior. These can range from slight alterations existing behaviors the establishment wholly novel behaviors. The biting observed Carpenter ants infected specialized fungus Ophiocordyceps unilateralis s.l. is an example latter. Though parasitic generally assumed be due parasite's gene expression, few studies have set out test this. We experimentally collect tissue both...