scholarly journals New Method for Identifying Fungal Kingdom Enzyme Hotspots from Genome Sequences

2021 ◽  
Vol 7 (3) ◽  
pp. 207
Author(s):  
Lene Lange ◽  
Kristian Barrett ◽  
Anne S. Meyer
Keyword(s):  
Fungal Species ◽  
Fungal Genome ◽  
Sequencing Data ◽  
Carbohydrate Active Enzymes ◽  
New Approach ◽  
Fungal Enzyme ◽  
Biomass Processing ◽  
Fungal Genomes ◽  
Robust Prediction ◽  
Fungal Kingdom

Fungal genome sequencing data represent an enormous pool of information for enzyme discovery. Here, we report a new approach to identify and quantitatively compare biomass-degrading capacity and diversity of fungal genomes via integrated function-family annotation of carbohydrate-active enzymes (CAZymes) encoded by the genomes. Based on analyses of 1932 fungal genomes the most potent hotspots of fungal biomass processing CAZymes are identified and ranked according to substrate degradation capacity. The analysis is achieved by a new bioinformatics approach, Conserved Unique Peptide Patterns (CUPP), providing for CAZyme-family annotation and robust prediction of molecular function followed by conversion of the CUPP output to lists of integrated “Function;Family” (e.g., EC 3.2.1.4;GH5) enzyme observations. An EC-function found in several protein families counts as different observations. Summing up such observations allows for ranking of all analyzed genome sequenced fungal species according to richness in CAZyme function diversity and degrading capacity. Identifying fungal CAZyme hotspots provides for identification of fungal species richest in cellulolytic, xylanolytic, pectinolytic, and lignin modifying enzymes. The fungal enzyme hotspots are found in fungi having very different lifestyle, ecology, physiology and substrate/host affinity. Surprisingly, most CAZyme hotspots are found in enzymatically understudied and unexploited species. In contrast, the most well-known fungal enzyme producers, from where many industrially exploited enzymes are derived, are ranking unexpectedly low. The results contribute to elucidating the evolution of fungal substrate-digestive CAZyme profiles, ecophysiology, and habitat adaptations, and expand the knowledge base for novel and improved biomass resource utilization.

Carbo-loading in Coccidioides spp.: a quantitative analysis of CAZyme abundance and resulting glycan populations

Glycobiology ◽  
2019 ◽  
Author(s):  
Natalie M Mitchell ◽  
Thomas E Grys ◽  
Douglas F Lake
Keyword(s):  
Pathogenic Fungi ◽  
Preliminary Evidence ◽  
American Southwest ◽  
Carbohydrate Active Enzymes ◽  
Diagnostic Approaches ◽  
Fungal Genomes ◽  
Species Specific ◽  
Fungal Kingdom

Abstract Coccidioides spp. are important pneumonia-causing pathogens of the American southwest, but little is known about their glycobiology and how their glycosylations differ from other pneumonia-causing fungi. There is mounting preliminary evidence to suggest genus or even species-specific glycosylations in the fungal kingdom due to the presence of unique Carbohydrate-Active Enzymes (CAZymes) in fungal genomes (Deshpande and others 2008; Karkowska-Kuleta and Kozik 2015). If Coccidioides spp.-specific glycans can be identified, it may be possible to exploit these differences to develop more specific diagnostic approaches and more effective therapeutics. Herein we i) mined Coccidioides spp. and other pathogenic fungal genomes to identify CAZymes specific for Coccidiodes spp., ii) proteomically determined the Coccidioides spp. “CAZome” produced in vivo and in vitro, and iii) utilized glycomics to differentiate Coccidioides genus-specific N-glycans from other pathogenic fungi. As far as we are aware, this is the first proteomic and glycomic comparison of the N-glycomes and CAZomes of different fungal genera during infection in human hosts.

scholarly journals Metabolomic Analysis of The Chemical Diversity of South Africa Leaf Litter Fungal Species Using an Epigenetic Culture-Based Approach

Molecules ◽  
2021 ◽  
Vol 26 (14) ◽  
pp. 4262
Author(s):  
Rachel Serrano ◽  
Víctor González-Menéndez ◽  
Germán Martínez ◽  
Clara Toro ◽  
Jesús Martín ◽  
...  
Keyword(s):  
South Africa ◽  
Genome Mining ◽  
Fungal Species ◽  
Chemical Diversity ◽  
Fermentation Conditions ◽  
Metabolite Profiles ◽  
Different Populations ◽  
Fungal Genomes ◽  
Microbial Natural Products ◽  
Fermentation Media

Microbial natural products are an invaluable resource for the biotechnological industry. Genome mining studies have highlighted the huge biosynthetic potential of fungi, which is underexploited by standard fermentation conditions. Epigenetic effectors and/or cultivation-based approaches have successfully been applied to activate cryptic biosynthetic pathways in order to produce the chemical diversity suggested in available fungal genomes. The addition of Suberoylanilide Hydroxamic Acid to fermentation processes was evaluated to assess its effect on the metabolomic diversity of a taxonomically diverse fungal population. Here, metabolomic methodologies were implemented to identify changes in secondary metabolite profiles to determine the best fermentation conditions. The results confirmed previously described effects of the epigenetic modifier on the metabolism of a population of 232 wide diverse South Africa fungal strains cultured in different fermentation media where the induction of differential metabolites was observed. Furthermore, one solid-state fermentation (BRFT medium), two classic successful liquid fermentation media (LSFM and YES) and two new liquid media formulations (MCKX and SMK-II) were compared to identify the most productive conditions for the different populations of taxonomic subgroups.

scholarly journals Nucleus-specific expression in the multinuclear mushroom-forming fungusAgaricus bisporusreveals different nuclear regulatory programs

2018 ◽  
Vol 115 (17) ◽  
pp. 4429-4434 ◽  
Author(s):  
Thies Gehrmann ◽  
Jordi F. Pelkmans ◽  
Robin A. Ohm ◽  
Aurin M. Vos ◽  
Anton S. M. Sonnenberg ◽  
...  
Keyword(s):  
Agaricus Bisporus ◽  
Sequencing Data ◽  
Carbohydrate Active Enzymes ◽  
Nuclear Level ◽  
Specific Expression ◽  
Phenotypic Differences ◽  
Gene Level ◽  
Nuclear Separation ◽  
Insight Into ◽  
Specific Mrna

Many fungi are polykaryotic, containing multiple nuclei per cell. In the case of heterokaryons, there are different nuclear types within a single cell. It is unknown what the different nuclear types contribute in terms of mRNA expression levels in fungal heterokaryons. Each cell of the mushroomAgaricus bisporuscontains two to 25 nuclei of two nuclear types originating from two parental strains. Using RNA-sequencing data, we assess the differential mRNA contribution of individual nuclear types and its functional impact. We studied differential expression between genes of the two nuclear types, P1 and P2, throughout mushroom development in various tissue types. P1 and P2 produced specific mRNA profiles that changed through mushroom development. Differential regulation occurred at the gene level, rather than at the locus, chromosomal, or nuclear level. P1 dominated mRNA production throughout development, and P2 showed more differentially up-regulated genes in important functional groups. In the vegetative mycelium, P2 up-regulated almost threefold more metabolism genes and carbohydrate active enzymes (cazymes) than P1, suggesting phenotypic differences in growth. We identified widespread transcriptomic variation between the nuclear types ofA. bisporus. Our method enables studying nucleus-specific expression, which likely influences the phenotype of a fungus in a polykaryotic stage. Our findings have a wider impact to better understand gene regulation in fungi in a heterokaryotic state. This work provides insight into the transcriptomic variation introduced by genomic nuclear separation.

scholarly journals Side-by-side analysis of alternative approaches on multi-level RNA-seq data

2017 ◽  
Author(s):  
Irina Mohorianu
Keyword(s):  
Differential Expression ◽  
Rna Seq ◽  
Sequencing Data ◽  
Essential Components ◽  
Sequencing Quality ◽  
Quality Checks ◽  
Multi Level ◽  
Using Data ◽  
Key Steps ◽  
Robust Prediction

AbstractBackgroundRNA sequencing (RNA-seq) is widely used for RNA quantification across environmental, biological and medical sciences; it enables the description of genome-wide patterns of expression and the deduction of regulatory interactions and networks. The aim of computational analyses is to achieve an accurate output, i.e. rigorous quantification of genes/transcripts to allow a reliable prediction of differential expression (DE), despite the variable levels of noise and biases present in sequencing data. The evaluation of sequencing quality and normalization are essential components of this process.ResultsWe investigate the discriminative power of existing approaches for the quality checking of mRNA-seq data and also propose additional, quantitative, quality checks. To accommodate the analysis of a nested, multi-level design using data on D. melanogaster, we incorporated the sample layout into the analysis. We describe a “subsampling without replacement”-based normalization and identification of DE that accounts for the experimental design i.e. the hierarchy and amplitude of effect sizes within samples. We also evaluate the differential expression call in comparison to existing approaches. To assess the broader applicability of these methods, we applied this series of steps to a published set of H. sapiens mRNA-seq samples.ConclusionsThe dataset-tailored methods improved sample comparability and delivered a robust prediction of subtle gene expression changes. Overall, the proposed approach offers the potential to improve key steps in the analysis of RNA-seq data by incorporating the structure and characteristics of biological experiments into the data analysis. 38

scholarly journals Below-ground plant–fungus network topology is not congruent with above-ground plant–animal network topology

2015 ◽  
Vol 1 (9) ◽  
pp. e1500291 ◽  
Author(s):  
Hirokazu Toju ◽  
Paulo R. Guimarães ◽  
Jens M. Olesen ◽  
John N. Thompson
Keyword(s):  
Network Topology ◽  
Network Architecture ◽  
Community Dynamics ◽  
Species Coexistence ◽  
Interspecific Interactions ◽  
Fungal Species ◽  
Sequencing Data ◽  
Phylogenetic Groups ◽  
Form Complex ◽  
Below Ground

In nature, plants and their pollinating and/or seed-dispersing animals form complex interaction networks. The commonly observed pattern of links between specialists and generalists in these networks has been predicted to promote species coexistence. Plants also build highly species-rich mutualistic networks below ground with root-associated fungi, and the structure of these plant–fungus networks may also affect terrestrial community processes. By compiling high-throughput DNA sequencing data sets of the symbiosis of plants and their root-associated fungi from three localities along a latitudinal gradient, we uncovered the entire network architecture of these interactions under contrasting environmental conditions. Each network included more than 30 plant species and hundreds of mycorrhizal and endophytic fungi belonging to diverse phylogenetic groups. The results were consistent with the notion that processes shaping host-plant specialization of fungal species generate a unique linkage pattern that strongly contrasts with the pattern of above-ground plant–partner networks. Specifically, plant–fungus networks lacked a “nested” architecture, which has been considered to promote species coexistence in plant–partner networks. Rather, the below-ground networks had a conspicuous “antinested” topology. Our findings lead to the working hypothesis that terrestrial plant community dynamics are likely determined by the balance between above-ground and below-ground webs of interspecific interactions.

scholarly journals BG7: A New Approach for Bacterial Genome Annotation Designed for Next Generation Sequencing Data

PLoS ONE ◽  
2012 ◽  
Vol 7 (11) ◽  
pp. e49239 ◽  
Author(s):  
Pablo Pareja-Tobes ◽  
Marina Manrique ◽  
Eduardo Pareja-Tobes ◽  
Eduardo Pareja ◽  
Raquel Tobes
Keyword(s):  
Next Generation Sequencing ◽  
Genome Annotation ◽  
Bacterial Genome ◽  
Next Generation Sequencing Data ◽  
Next Generation ◽  
Sequencing Data ◽  
New Approach ◽  
Generation Sequencing

scholarly journals Conservation of griseofulvin genes in the gsf gene cluster among fungal genomes

2021 ◽  
Author(s):  
Parisa Aris ◽  
Lihong Yan ◽  
Yulong Wei ◽  
Ying Chang ◽  
Bihong Shi ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Biosynthetic Gene Cluster ◽  
Fungal Species ◽  
Antifungal Compound ◽  
Biosynthetic Gene ◽  
Polyketide Biosynthesis ◽  
Third Generation Sequencing ◽  
Penicillium Griseofulvum ◽  
Fungal Genomes ◽  
Generation Sequencing

Abstract The polyketide griseofulvin is a natural antifungal compound and research in griseofulvin has been key in establishing our current understanding of polyketide biosynthesis. Nevertheless, the griseofulvin gsf biosynthetic gene cluster (BGC) remains poorly understood in most fungal species, including Penicillium griseofulvum where griseofulvin was first isolated. To elucidate essential genes involved in griseofulvin biosynthesis, we performed third-generation sequencing to obtain the genome of Penicillium griseofulvum strain D-756. Furthermore, we gathered publicly available genome of 11 other fungal species in which gsf gene cluster was identified. In a comparative genome analysis, we annotated and compared the gsf BGC of all 12 fungal genomes. Our findings show no gene rearrangements at the gsf BGC. Furthermore, seven gsf genes are conserved by most genomes surveyed whereas the remaining six were poorly conserved. This study provides new insights into differences between gsf BGC and suggests that seven gsf genes are essential in griseofulvin production.

scholarly journals Yanocomp: robust prediction of m6A modifications in individual nanopore direct RNA reads.

2021 ◽  
Author(s):  
Matthew T Parker ◽  
Geoffrey J Barton ◽  
Gordon G Simpson
Keyword(s):  
Rna Sequencing ◽  
Mixture Models ◽  
Single Molecule ◽  
Rna Processing ◽  
Sequencing Data ◽  
Rna Modifications ◽  
Robust Prediction ◽  
Good Support

Yanocomp is a tool for predicting the positions and stoichiometries of RNA modifications in Nanopore direct RNA sequencing data. It uses general mixture models to identify differentially modified sites between two conditions, with good support for replicates. Yanocomp models across adjacent kmers and uses a uniform component to account for outliers, improving the accuracy of single molecule predictions. Consequently, Yanocomp can be used to measure modification stoichiometry, and correlate modifications with other RNA processing events. Yanocomp is available under an MIT license at www.github.com/bartongroup/yanocomp.

scholarly journals Giant Starship elements mobilize accessory genes in fungal genomes

2021 ◽  
Author(s):  
Emile Gluck-Thaler ◽  
Timothy Ralston ◽  
Zachary Konkel ◽  
Cristhian Grabowski Ocampos ◽  
Veena Devi Ganeshan ◽  
...  
Keyword(s):  
Genome Structure ◽  
5S Rdna ◽  
Macrophomina Phaseolina ◽  
Fungal Species ◽  
Mobile Elements ◽  
Integrative And Conjugative Elements ◽  
Standing Variation ◽  
Accessory Genes ◽  
Fungal Genomes ◽  
The Impact

Accessory genes are variably present among members of a species and are a reservoir of adaptive functions. In bacteria, differences in gene distributions among individuals largely result from mobile elements that acquire and disperse accessory genes as cargo. In contrast, the impact of cargo-carrying elements on eukaryotic evolution remains largely unknown. Here, we show that variation in genome content within multiple fungal species is facilitated by Starships, a novel group of massive mobile elements that are 110 kb long on average, share conserved components, and carry diverse arrays of accessory genes. We identified hundreds of Starship-like regions across every major class of filamentous Ascomycetes, including 28 distinct Starships that range from 27-393 kb and last shared a common ancestor ca. 400 mya. Using new long-read assemblies of the plant pathogen Macrophomina phaseolina, we characterize 4 additional Starships whose past and ongoing activities contribute to standing variation in genome structure and content. One of these elements, Voyager, inserts into 5S rDNA and contains a candidate virulence factor whose increasing copy number has contrasting associations with pathogenic and saprophytic growth, suggesting Voyager activity underlies an ecological trade-off. We propose that Starships are eukaryotic analogs of bacterial integrative and conjugative elements based on parallels between their conserved components and may therefore represent the first known agents of active gene transfer in eukaryotes. Our results suggest that Starships have shaped the content and structure of fungal genomes for millions of years and reveal a new concerted route for evolution throughout an entire eukaryotic phylum.

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