Mushroom-forming fungi
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ABSTRACT:
PROVIDER: PRJNA1120350 | ENA |
REPOSITORIES: ENA
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Project description:An evolutionarily ancient transcription factor drives spore morphogenesis in mushroom-forming fungi
| PRJNA1123746 | ENA
Project description:Mushroom-forming fungi (Agaricomycetes) are emerging as pivotal players in several fields, as drivers of nutrient cycling, sources of novel applications, or as the group that includes the most morphologically complex fungi. Genomic data for Agaricomycetes are accumulating at a steady pace, however, this is not paralleled by improvements in the quality of genome sequence and associated functional gene annotations, which leaves gene function notoriously poorly understood in comparison with other fungi and model eukaryotes. We set out to improve our functional understanding of the model mushroom Coprinopsis cinerea by integrating a new, chromosome-level assembly with high-quality gene predictions and functional information derived from gene-expression profiling data across 67 developmental, stress, and light conditions. The new annotation includes 5′- and 3′-untranslated regions (UTRs), polyadenylation sites (PAS), upstream ORFs (uORFs), splicing isoforms, conserved sequence motifs (e.g., TATA and Kozak boxes) and microexons. We found that alternative polyadenylation is widespread in C. cinerea, but that it is not specifically regulated across the various conditions used here. Transcriptome profiling allowed us to delineate core gene sets corresponding to carbon starvation, light-response, and hyphal differentiation, and uncover new aspects of the light-regulated phases of life cycle. As a result, the genome of C. cinerea has now become the most comprehensively annotated genome among mushroom-forming fungi, which will contribute to multiple rapidly expanding fields, including research on their life history, light and stress responses, as well as multicellular development.
2025-01-30 | GSE287886 | GEO
Project description:The evolution of complex multicellularity has been one of the major transitions in the history of life. In contrast to simple multicellular aggregates of cells, it has evolved only in a handful of lineages, including the animals, embryophytes, red and brown algae and fungi. Despite being a key step towards the evolution of complex organisms, the evolutionary origins and the genetic underpinnings of complex multicellularity are incompletely known. We constructed a reference atlas of mushroom formation based on developmental transcriptome data of six species and comparisons of >200 whole genomes, to elucidate the core genetic program of complex multicellularity and fruiting body development in mushroom-forming fungi (Agaricomycetes). Nearly 300 conserved gene families and >70 functional groups contained developmentally regulated genes from five to six species, covering functions related to fungal cell wall (FCW) remodeling, targeted protein degradation, signal transduction, adhesion and small secreted proteins (including effector-like orphan genes). Several of these families, including F-box proteins, expansin-like proteins, protein kinases, and transcription factors, showed expansions in Agaricomycetes, with from which many convergently expandedwere identified in multicellular plants and/or animals too, assuming convergent solutions to genetic hurdles imposed by complex multicellularity among independently evolved lineages. This study provides a novel entry point to studying mushroom development and complex multicellularity in one of the largest clades of complex eukaryotic organisms.
2019-03-16 | GSE125199 | GEO
Project description:The evolution of complex multicellularity has been one of the major transitions in the history of life. In contrast to simple multicellular aggregates of cells, it has evolved only in a handful of lineages, including the animals, embryophytes, red and brown algae and fungi. Despite being a key step towards the evolution of complex organisms, the evolutionary origins and the genetic underpinnings of complex multicellularity are incompletely known. We constructed a reference atlas of mushroom formation based on developmental transcriptome data of six species and comparisons of >200 whole genomes, to elucidate the core genetic program of complex multicellularity and fruiting body development in mushroom-forming fungi (Agaricomycetes). Nearly 300 conserved gene families and >70 functional groups contained developmentally regulated genes from five to six species, covering functions related to fungal cell wall (FCW) remodeling, targeted protein degradation, signal transduction, adhesion and small secreted proteins (including effector-like orphan genes). Several of these families, including F-box proteins, expansin-like proteins, protein kinases, and transcription factors, showed expansions in Agaricomycetes, with from which many convergently expandedwere identified in multicellular plants and/or animals too, assuming convergent solutions to genetic hurdles imposed by complex multicellularity among independently evolved lineages. This study provides a novel entry point to studying mushroom development and complex multicellularity in one of the largest clades of complex eukaryotic organisms.
2019-03-16 | GSE125195 | GEO
Project description:The evolution of complex multicellularity has been one of the major transitions in the history of life. In contrast to simple multicellular aggregates of cells, it has evolved only in a handful of lineages, including the animals, embryophytes, red and brown algae and fungi. Despite being a key step towards the evolution of complex organisms, the evolutionary origins and the genetic underpinnings of complex multicellularity are incompletely known. We constructed a reference atlas of mushroom formation based on developmental transcriptome data of six species and comparisons of >200 whole genomes, to elucidate the core genetic program of complex multicellularity and fruiting body development in mushroom-forming fungi (Agaricomycetes). Nearly 300 conserved gene families and >70 functional groups contained developmentally regulated genes from five to six species, covering functions related to fungal cell wall (FCW) remodeling, targeted protein degradation, signal transduction, adhesion and small secreted proteins (including effector-like orphan genes). Several of these families, including F-box proteins, expansin-like proteins, protein kinases, and transcription factors, showed expansions in Agaricomycetes, with from which many convergently expandedwere identified in multicellular plants and/or animals too, assuming convergent solutions to genetic hurdles imposed by complex multicellularity among independently evolved lineages. This study provides a novel entry point to studying mushroom development and complex multicellularity in one of the largest clades of complex eukaryotic organisms.
2019-03-16 | GSE125190 | GEO
Project description:The evolution of complex multicellularity has been one of the major transitions in the history of life. In contrast to simple multicellular aggregates of cells, it has evolved only in a handful of lineages, including the animals, embryophytes, red and brown algae and fungi. Despite being a key step towards the evolution of complex organisms, the evolutionary origins and the genetic underpinnings of complex multicellularity are incompletely known. We constructed a reference atlas of mushroom formation based on developmental transcriptome data of six species and comparisons of >200 whole genomes, to elucidate the core genetic program of complex multicellularity and fruiting body development in mushroom-forming fungi (Agaricomycetes). Nearly 300 conserved gene families and >70 functional groups contained developmentally regulated genes from five to six species, covering functions related to fungal cell wall (FCW) remodeling, targeted protein degradation, signal transduction, adhesion and small secreted proteins (including effector-like orphan genes). Several of these families, including F-box proteins, expansin-like proteins, protein kinases, and transcription factors, showed expansions in Agaricomycetes, with from which many convergently expandedwere identified in multicellular plants and/or animals too, assuming convergent solutions to genetic hurdles imposed by complex multicellularity among independently evolved lineages. This study provides a novel entry point to studying mushroom development and complex multicellularity in one of the largest clades of complex eukaryotic organisms.
2019-03-16 | GSE125184 | GEO
Project description:The evolution of complex multicellularity has been one of the major transitions in the history of life. In contrast to simple multicellular aggregates of cells, it has evolved only in a handful of lineages, including the animals, embryophytes, red and brown algae and fungi. Despite being a key step towards the evolution of complex organisms, the evolutionary origins and the genetic underpinnings of complex multicellularity are incompletely known. We constructed a reference atlas of mushroom formation based on developmental transcriptome data of six species and comparisons of >200 whole genomes, to elucidate the core genetic program of complex multicellularity and fruiting body development in mushroom-forming fungi (Agaricomycetes). Nearly 300 conserved gene families and >70 functional groups contained developmentally regulated genes from five to six species, covering functions related to fungal cell wall (FCW) remodeling, targeted protein degradation, signal transduction, adhesion and small secreted proteins (including effector-like orphan genes). Several of these families, including F-box proteins, expansin-like proteins, protein kinases, and transcription factors, showed expansions in Agaricomycetes, with from which many convergently expandedwere identified in multicellular plants and/or animals too, assuming convergent solutions to genetic hurdles imposed by complex multicellularity among independently evolved lineages. This study provides a novel entry point to studying mushroom development and complex multicellularity in one of the largest clades of complex eukaryotic organisms.
2019-03-16 | GSE125198 | GEO
Project description:During mycoparasitism, a fungus—the host—is parasitized by another fungus—the mycoparasite. The genetic underpinnings of these relationships have been best characterized in Ascomycete fungi. However, within Basidiomycete fungi, there are rare instances of mushroom-forming species parasitizing the reproductive structures, or sporocarps, of other mushroom-forming species. One of the most enigmatic of these occurs between Entoloma abortivum and species of Armillaria, where hyphae of E. abortivum are hypothesized to disrupt the development of Armillaria sporocarps, resulting in the formation of carpophoroids. However, it remains unknown whether carpophoroids are the direct result of a mycoparasitic relationship. To address the nature of this unique interaction, we analyzed gene expression of field-collected Armillaria and E. abortivum sporocarps and carpophoroids. Transcripts in the carpophoroids are primarily from E. abortivum, supporting the hypothesis that this species is parasitizing Armillaria. Most notably, we identified differentially expressed E. abortivum β-trefoil-type lectins in the carpophoroid, which we hypothesize bind to Armillaria cell wall galactomannoproteins, thereby mediating recognition between the mycoparasite and the host. The most significantly upregulated E. abortivum transcripts in the carpophoroid code for oxalate decarboxylases—enzymes that degrade oxalic acid. Oxalic acid is a virulence factor in many plant pathogens, including Armillaria species, however, E. abortivum has evolved a sophisticated strategy to overcome this defense mechanism. The number of gene models and genes that code for carbohydrate-active enzymes in the E. abortivum transcriptome were reduced compared to other closely related species, perhaps as a result of the specialized nature of this interaction.
2021-09-23 | GSE183699 | GEO
Project description:Sporulation is the most widespread means of reproduction and dispersal in fungi and, at the same time, an industrially important trait in crop mushrooms. In the Basidiomycota, sexual spores are produced on specialized cells known as basidia, from which they are forcibly discharged with the highest known acceleration in nature. However, the genetics of sporulation remains poorly known. Here, we identify a new, highly conserved transcription factor, sporulation-related regulator 1 (srr1), and systematically address the genetics of spore formation for the first time in the Basidiomycota. We show that Srr1 regulates postmeiotic spore morphogenesis, but not other aspects of fruiting body development or meiosis, and its role is conserved in the phylogenetically distant, but industrially important, Pleurotus spp. (oyster mushrooms). We used RNA sequencing to understand genes directly or indirectly regulated by Srr1 and identified a strongly supported binding motif for the protein. Using an inferred network of putative target genes regulated by Srr1 and comparative genomics, we identified genes lost in secondarily non-ballistosporic taxa, including a novel sporulation-specific chitinase gene. Overall, our study offers systematic insights into the genetics of spore morphogenesis in the Basidiomycota.
2025-02-26 | GSE269820 | GEO
Project description:One new order, one new family, and one new combination are presented, as the result of molecular phylogenetic analyses. The new order Stereopsidales and the new family Stereopsidaceae are described incorporating Stereopsis radicans and S. globosa, formerly Clavulicium globosum. We show that not only do these species represent an old overlooked lineage, but both species harbor cryptic diversity. In addition, a third species, C. macounii, appears as a plausible sister to the new lineage, but there is conflict in the data. All specimens of S. radicans and S. globosa analysed here are from the South and Central Americas; several records of S. radicans have been made also from tropical Asia. We expect the true diversity in this group to be a lot higher than presented in this paper. Stereopsis radicans was formerly included in Polyporales, but a placement within that order is rejected by our data through SH tests. The dataset consisted of four nuclear markers: rpb2, tef1, LSU and SSU, each of which was analysed separately using maximum likelihood and Bayesian inference. Recombination detection tests indicate no plausible recombinations. The potential of S. radicans, S. globosa and C. macounii being amphitallic is briefly discussed.
| S-EPMC4002437 | biostudies-literature