Evolution and comparative genomics of the most common Trichoderma species

BMC Genomics, Journal Year: 2019, Volume and Issue: 20(1)

Published: June 12, 2019

The growing importance of the ubiquitous fungal genus Trichoderma (Hypocreales, Ascomycota) requires understanding its biology and evolution. Many species are used as biofertilizers biofungicides T. reesei is model organism for industrial production cellulolytic enzymes. In addition, some highly opportunistic devastate mushroom farms can become pathogens humans. A comparative analysis first three whole genomes revealed mycoparasitism innate feature Trichoderma. However, evolution these traits not yet understood.

Language: Английский

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Massive lateral transfer of genes encoding plant cell wall-degrading enzymes to the mycoparasitic fungus Trichoderma from its plant-associated hosts

PLoS Genetics, Journal Year: 2018, Volume and Issue: 14(4), P. e1007322 - e1007322

Published: April 9, 2018

Unlike most other fungi, molds of the genus Trichoderma (Hypocreales, Ascomycota) are aggressive parasites fungi and efficient decomposers plant biomass. Although nutritional shifts common among hypocrealean there no examples such broad substrate versatility as that observed in Trichoderma. A phylogenomic analysis 23 (including nine spp. related Escovopsis weberi) revealed has evolved from an ancestor with limited cellulolytic capability fed on either or arthropods. The evolutionary genes encoding cell wall-degrading carbohydrate-active enzymes auxiliary proteins (pcwdCAZome, 122 gene families) based a tree / species reconciliation demonstrated formation was accompanied by unprecedented extent lateral transfer (LGT). Nearly one-half pcwdCAZome (41%) were obtained via LGT plant-associated filamentous belonging to different classes Ascomycota, while potential donors. In addition ability feed unrelated (such Basidiomycota), we also showed is capable endoparasitism range including extant This phenomenon not E. weberi rarely mycoparasitic fungi. Thus, our study suggests linked parasitize taxonomically (up adelphoparasitism strict sense). may have allowed primarily mycotrophic evolve into

Language: Английский

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Distinct roles of N- and O-glycans in cellulase activity and stability

Proceedings of the National Academy of Sciences, Journal Year: 2017, Volume and Issue: 114(52), P. 13667 - 13672

Published: Dec. 11, 2017

Significance Glycosylation is a ubiquitous posttranslational modification of proteins wherein carbohydrates are appended to protein side chains, with myriad functions in molecular and cell biology. The enzymes that break down polysaccharides other recalcitrant polymers nature often decorated two canonical forms glycosylation, N- O-linked glycans, the roles which only partially understood these key enzyme families importance both natural biomass turnover industrial biotechnology. Here, we report that, depending on where they attached, glycans play substantially different for thermal proteolytic stability, substrate binding, turnover. Overall, results provide fundamental insights into how affect critical properties biomass-degrading enzymes.

Language: Английский

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Repeat elements organise 3D genome structure and mediate transcription in the filamentous fungus Epichloë festucae

PLoS Genetics, Journal Year: 2018, Volume and Issue: 14(10), P. e1007467 - e1007467

Published: Oct. 24, 2018

Structural features of genomes, including the three-dimensional arrangement DNA in nucleus, are increasingly seen as key contributors to regulation gene expression. However, studies on how genome structure and nuclear organisation influence transcription have so far been limited a handful model species. This narrow focus limits our ability draw general conclusions about ways which structures encoded, integrate information from data address broader gamut biological questions. Here, we generate complete gapless sequence for filamentous fungus, Epichloë festucae. We use Hi-C examine genome, RNA-seq investigate contributes suite transcriptional changes needed maintain symbiotic relationships with grass host. Our results reveal very repeat-rich blocks discrete boundaries interspersed by gene-rich sequences that almost repeat-free. In contrast other species reported date, is anchored these repeat blocks, act isolate neighbouring regions. Genes differentially expressed planta enriched near suggesting their orientation partly encodes regulates relationship formed this organism.

Language: Английский

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The RIPper, a web-based tool for genome-wide quantification of Repeat-Induced Point (RIP) mutations

PeerJ, Journal Year: 2019, Volume and Issue: 7, P. e7447 - e7447

Published: Aug. 26, 2019

The RIPper (http://theripper.hawk.rocks) is a set of web-based tools designed for analyses Repeat-Induced Point (RIP) mutations in the genome sequences Ascomycota. RIP pathway fungal defense mechanism that aimed at identifying repeated and duplicated motifs, into which it then introduces cytosine to thymine transition mutations. thus serves deactivate counteract deleterious consequences selfish or mobile DNA elements genomes. occurrence, genetic context frequency are widely used assess activity this genomic regions interest. Here, we present bioinformatics tool specifically fashioned automate investigation changes product substrate nucleotide frequencies genomes.We demonstrated ability detect occurrence extent known affected sequences. Specifically, sliding window approach was perform genome-wide analysis on assembly Neurospora crassa. Additionally, fine-scale with showed gene transposable element sequences, previously determined be by RIP, were indeed characterized high Data generated using software further large proportions N. crassa constitutes extensively displaying reduced GC content. useful investigating visualizing across length interest, allowing analyses.This identified targeted provided statistics an entire assembly, including proportion RIP. as efficient analyses.

Language: Английский

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Genome-Wide Analyses of Repeat-Induced Point Mutations in the Ascomycota

Frontiers in Microbiology, Journal Year: 2021, Volume and Issue: 11

Published: Feb. 1, 2021

The Repeat-Induced Point (RIP) mutation pathway is a fungus-specific genome defense mechanism that mitigates the deleterious consequences of repeated genomic regions and transposable elements (TEs). RIP mutates targeted sequences by introducing cytosine to thymine transitions. We investigated genome-wide occurrence extent with sliding-window approach. Using data two sets control groups, association between RIP, TEs, GC content were contrasted in organisms capable incapable RIP. Based on these data, we then set out determine 58 representatives Ascomycota. findings summarized placing each fungi one six categories based In silico analyses, using approach stringent parameters, implemented simultaneously within same genetic context, high quality assemblies, yielded superior results determining among Most Ascomycota had mutations particularly widespread classes Pezizomycotina, including early diverging Orbiliomycetes Pezizomycetes. most extreme cases limited Dothideomycetes Sordariomycetes. By contrast, genomes Taphrinomycotina Saccharomycotina contained no detectable evidence Also, recent losses combined controlled TE proliferation Pezizomycotina subphyla may promote substantial enlargement as well formation sub-genomic compartments. These have broadened our understanding taxonomic range how this affects harboring it.

Language: Английский

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Evaluation of antifungal, phosphate solubilisation, and siderophore and chitinase release activities of endophytic fungi from Pistacia vera

Mycological Progress, Journal Year: 2017, Volume and Issue: 16(8), P. 777 - 790

Published: June 21, 2017

Language: Английский

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Genome Sequencing and Carbohydrate-Active Enzyme (CAZyme) Repertoire of the White Rot Fungus Flammulina elastica

International Journal of Molecular Sciences, Journal Year: 2018, Volume and Issue: 19(8), P. 2379 - 2379

Published: Aug. 13, 2018

Next-generation sequencing (NGS) of the Flammulina elastica (wood-rotting basidiomycete) genome was performed to identify carbohydrate-active enzymes (CAZymes). The resulting assembly (31 kmer) revealed a total length 35,045,521 bp (49.7% GC content). Using AUGUSTUS tool, 12,536 gene structures were predicted by ab initio prediction. An analysis orthologs that 6806 groups contained at least one F. protein. Among genes, 24 species-specific which 17 genes paralogous. CAZymes are divided into five classes: glycoside hydrolases (GHs), carbohydrate esterases (CEs), polysaccharide lyases (PLs), glycosyltransferases (GTs), and auxiliary activities (AA). In present study, annotation amino acid sequences from using dbCAN CAZyme database 508 CAZymes, including 82 AAs, 218 GHs, 89 GTs, 18 PLs, 59 CEs, 42 binding modules in genome. Although repertoire similar those other fungal species, number GTs larger than basidiomycetes. This information elucidates newly identified wood-degrading machinery elastica, offers opportunities better understand this fungus, presents possibilities for more detailed studies on lignocellulosic biomass degradation may lead future biotechnological industrial applications.

Language: Английский

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A light life together: photosensing in the plant microbiota

Photochemical & Photobiological Sciences, Journal Year: 2021, Volume and Issue: 20(3), P. 451 - 473

Published: March 1, 2021

Bacteria and fungi of the plant microbiota can be phytopathogens, parasites or symbionts that establish mutually advantageous relationships with plants. They are often rich in photoreceptors for UVA-Visible light, many cases, they exhibit light regulation growth patterns, infectivity virulence, reproductive traits, production pigments metabolites. In addition to light-driven effects, demonstrated via generation photoreceptor gene knock-outs, microbial exert effects also dark. Interestingly, some switch their attitude towards plants dependence illumination dark conditions as much may symbiotic pathogenic. This review summarizes current knowledge about roles plant-associated bacteria aiming at identification common traits general working ideas. Still, reports on infection restricted description macroscopically observable phenomena, whereas detailed information molecular level, e.g., protein-protein interaction during signal transduction induction mechanisms infectivity/virulence initiation remains sparse. As it becomes apparent from still only few studies, photoreceptors, red- blue sensitive groups interact modulate individual effects. The topic is great relevance, even economic terms, referring plant-pathogen plant-symbionts interactions, considering increasing usage artificial greenhouses, possible light-regulation synthesis plant-growth stimulating substances herbicides by certain symbionts, biocontrol pests selected a sustainable agriculture.

Language: Английский

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The Sugar Metabolic Model of Aspergillus niger Can Only Be Reliably Transferred to Fungi of Its Phylum

Journal of Fungi, Journal Year: 2022, Volume and Issue: 8(12), P. 1315 - 1315

Published: Dec. 17, 2022

Fungi play a critical role in the global carbon cycle by degrading plant polysaccharides to small sugars and metabolizing them as energy sources. We mapped well-established sugar metabolic network of Aspergillus niger five taxonomically distant species (Aspergillus nidulans, Penicillium subrubescens, Trichoderma reesei, Phanerochaete chrysosporium Dichomitus squalens) using an orthology-based approach. The diversity metabolism correlates well with taxonomic distance fungi. pathways are highly conserved between three studied Eurotiomycetes (A. niger, A. P. subrubescens). A higher level was observed T. reesei even more so for two Basidiomycetes. These results were confirmed integrative analysis transcriptome, proteome metabolome, growth profiles fungi growing on corresponding sugars. In conclusion, establishment pathway models different revealed fungal conversion provided valuable resource community, which would facilitate rational engineering these microbial cell factories.

Language: Английский

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