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Analysis of metagenome for fungal community of soil under Tricholoma matsutake’s fruiting body.

ABSTRACT: Analysis of metagenome for fungal community of soil under Tricholoma matsutake’s fruiting body.

PROVIDER: PRJEB42318 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR5036870.fastq.gz	Fastqsanger.gz
	ERR5036880.fastq.gz	Fastqsanger.gz
	ERR5036871.fastq.gz	Fastqsanger.gz
	ERR5036881.fastq.gz	Fastqsanger.gz
	ERR5036872.fastq.gz	Fastqsanger.gz

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Comparative genomics reveals unique wood-decay strategies and fruiting body development in the Schizophyllaceae

Project description:Agaricomycetes produce the most efficient enzyme systems to degrade wood and the most complex morphological structures in the fungal kingdom. Despite decades-long interest in their genetic bases, the evolution and functional diversity of both wood-decay and fruiting body formation are incompletely known.Here, we perform comparative genomic and transcriptomic analyses of wood-decay and fruiting body development in Auriculariopsis ampla and Schizophyllum commune (Schizophyllaceae), species with secondarily simplified morphologies and enigmatic wood-decay strategy and weak pathogenicity to woody plants. The plant cell wall degrading enzyme repertoires of Schizophyllaceae are transitional between those of white rot species and less efficient wood-degraders such as brown rot or mycorrhizal fungi. Rich repertoires of suberinase and tannase genes were found in both species, with tannases restricted to Agaricomycetes that preferentially colonize bark-covered wood, suggesting potential complementation of their weaker wood-decaying abilities and adaptations to wood colonization through the bark. Fruiting body transcriptomes of A. ampla and S. commune revealed a high rate of divergence in developmental gene expression, but also several genes with conserved developmental expression, including novel transcription factors and small-secreted proteins, some of the latter might represent fruiting body effectors. Taken together, our analyses highlighted novel aspects of wood-decay and fruiting body development in a widely distributed family of mushroom-forming fungi.

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Heterobasidion fruiting body, woody material, soil

Project description:Heterobasidion fruiting body, heterobasidion infected woody tissue and adhering soil fungal community

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Homeobox transcription factors involved in fruiting body development of Volvariella volvacea

Project description:The genome of V. volvacea revealed 47 genes encoding homeobox transcription factors. Of them, 8 differentially expressed homeobox transcription factors were obtained by comparing the gene expression during primordia and elongation formation. Furthermore, quantitative real-time PCR was performed on selected genes with different expression levels to demonstrate the utility of digital gene expression for gene expression profiles during fruiting body formation. The results showed that five homeobox transcription factors were up-regulated during primordia formation, and three homeobox transcription factors were down-regulated from the egg stage to elongation stage. Overall, a critical role for homeobox transcription factor was believed to contribute to the fruiting body formation. Using the 3'-tag digital gene expression (DGE), we compared the gene expression profiles in fruiting body development of V. volvacea.

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Snowball-like mushroom morphologies and a novel gene family required for fruiting body development

Project description:The morphogenesis of sexual fruiting bodies of fungi is a complex process determined by a genetically encoded programme. Fruiting bodies reached highest complexity levels in the Agaricomycetes, yet, the underlying genetics is currently poorly known. In this work, we functionally characterised an unannotated gene we term snb1, whose expression level increases rapidly during fruiting body initiation. According to phylogenetic analyses, orthologues of snb1 are present in almost all Agaricomycetes and may represent a novel conserved gene family that plays a substantial role in fruiting body development. We disrupted snb1 using CRISPR/Cas9 in the agaricomycete model organism Coprinopsis cinerea. Snb1 mutants formed unique, snowball-shaped, rudimentary fruiting bodies that could not differentiate caps, stipes and lamellae. We took advantage of this phenotype to study fruiting body differentiation using RNA-Seq analyses. This revealed a multitude of differentially regulated genes and gene families that may be related to tissue differentiation and the formation of structures. Taken together, the novel gene family of snb1 and the differentially expressed genes in the snb1 mutants provide valuable insights into the complex mechanisms underlying tissue differentiation in the Agaricomycetes.

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Homeobox transcription factors involved in fruiting body development of Volvariella volvacea

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Transcriptional profiling elucidates the essential role of glycogen synthase kinase 3 to fruiting body formation in Coprinopsis cinerea

Project description:We used high-throughput RNA sequencing (RNA-Seq) to reveal the transcriptional response of C. cinerea on fruiting body formation and development with GSK3 inhibited by the addition of LiCl. The transcriptional profile revealed could elucidate the role of GSK3 activity in fruiting body development.

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5'-Serial Analysis of Gene Expression of the transcriptomes of Coprinopsis cinerea during fruiting body initiation

Project description:Large scale assessment of the transcriptomes of the vegetative mycelium and primordium will facilitate the generation of a more comprehensive picture of the fruiting process in basidiomycetes. We coupled 5'-Serial Analysis of Gene Expression (5'-SAGE) to high-throughput pyrosequencing from 454 Life Sciences to analyze the transcriptomes and identify up-regulated genes (URGs) among vegetative mycelium (Myc) and stage 1 primordium (S1-Pri) of Coprinopsis cinerea during fruiting body development. We evaluated the expression of >3,000 genes in the two respective growth stages and demonstrated that almost one-third of these genes were preferentially expressed in either stage, which implicated a significant transcriptomic switch during fruiting body initiation. We annotated >34,000 and >45,000 transcription start sites (TSSs) in the transcriptomes of Myc and S1-Pri respectively. We identified a wealth of potential URGs related to early fruiting events, although their functions and roles are not exactly known. This study serves to advance our understanding of the molecular mechanisms of fruiting body development in the model mushroom C. cinerea.

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5'-Serial Analysis of Gene Expression of the transcriptomes of Coprinopsis cinerea during fruiting body initiation

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mRNA-seq and miRNA-seq profiling analyses reveal molecular mechanisms regulating induction of fruiting bodies in Ophiocordyceps Sinensis [miRNA-seq dataset]

Project description:Ophiocordyceps sinensis (Berk.) Sacc., a complex of larval carcass (sclerotium) and stroma formed by the fungus of Hirsutella sinensis infecting Hepialidae insect larvae, whose fruiting body is also the main fungal structure used for taxonomic identification. However, the induction of fruiting body is still inefficient and the high cost resulting in the large-scale artificial cultivation of this fungus has been unsuccessful in China.In this study,important factors and target genes associated with the fruiting body induction during the development of O. sinensis were identified, providing a basic molecular mechanism for facilitating the large-scale artificial cultivation of O. sinensis.

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mRNA-seq and miRNA-seq profiling analyses reveal molecular mechanisms regulating induction of fruiting bodies in Ophiocordyceps Sinensis [mRNA-seq dataset]

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