Marine metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1178733 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Comparative genomics of saprotrophic, endophytic and pathogenic Fusarium species
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Project description:Comparative genomics of saprotrophic, endophytic, and pathogenic species of the family Marasmiaceae
| PRJNA992404 | ENA
Project description:The genus Armillaria spp. (Fungi, Basidiomycota) includes devastating pathogens of temperate forests and saprotrophs that decay wood. Pathogenic and saprotrophic Armillaria species can efficiently colonize and decay woody substrates, however, mechanisms of wood penetration and colonization are poorly known. We assayed the colonization and decay of autoclaved spruce roots using the conifer-specialists Armillaria ostoyae and A. cepistipes using transcriptomic and proteomic data. Transcript and protein levels were altered more extensively in the saprotrophic A. cepistipes than in the pathogenic A. ostoyae and in invasive mycelia of both species compared to their rhizomorphs. Diverse suites of carbohydrate-active enzyme genes (CAZymes), in particular pectinolytic ones and expansins, were upregulated in both species, whereas ligninolytic genes were mostly downregulated. Our gene expression data, together with previous comparative genomic and decay-chemistry analyses suggest that wood decay by Armillaria differs from that of typical white rot fungi and shows features resembling soft rot. We propose that Armillaria species have modified the ancestral white rot machinery so that it allows for selective ligninolysis based on environmental conditions and/or host types.
2020-05-04 | GSE149701 | GEO
Project description:The genus Armillaria spp. (Fungi, Basidiomycota) includes devastating pathogens of temperate forests and saprotrophs that decay wood. Pathogenic and saprotrophic Armillaria species can efficiently colonize and decay woody substrates, however, mechanisms of wood penetration and colonization are poorly known. We assayed the colonization and decay of autoclaved spruce roots using the conifer-specialists Armillaria ostoyae and A. cepistipes using transcriptomic and proteomic data. Transcript and protein levels were altered more extensively in the saprotrophic A. cepistipes than in the pathogenic A. ostoyae and in invasive mycelia of both species compared to their rhizomorphs. Diverse suites of carbohydrate-active enzyme genes (CAZymes), in particular pectinolytic ones and expansins, were upregulated in both species, whereas ligninolytic genes were mostly downregulated. Our gene expression data, together with previous comparative genomic and decay-chemistry analyses suggest that wood decay by Armillaria differs from that of typical white rot fungi and shows features resembling soft rot. We propose that Armillaria species have modified the ancestral white rot machinery so that it allows for selective ligninolysis based on environmental conditions and/or host types.
2020-05-04 | GSE149725 | GEO
Project description:Conidial germination marks the beginning of the fungal life cycle, and understanding the genes associated with conidial germination provides insights into fungal pathogenicity and host interactions. Here, we use comparative transcriptomics to demonstrate the transcriptional similarities and differences during conidial germination and initial colony establishment in a plant pathogenic and an endophytic fungus, Fusarium graminearum and M. anisopliae, respectively. We compared the transcriptomes of F. graminearum and M. anisopliae across four stages of conidial germination: fresh conidia, polar growth, hyphal extension, and either first hyphal branching (on medium) or appressorium formation (on barley). F. graminearum exhibited a higher upregulation of CAZyme, specialized metabolite and effector genes compared to M. anisopliae during interaction with the host, particularly in the appressorium stage, reflecting its pathogenic nature. The appressorium structures formed when M. anisopliae conidia germinated on the host. The transcriptome analysis revealed that the fungus produced reduced transcript levels of CAZyme and specialized metabolite genes reflecting a less aggressive host penetration approach. The candidate genes associated with IAA synthesis were upregulated in M. anisopliae during the appressorium stage, supporting its endophytic lifestyle and suggests that the fungus uses a phytohormone based strategy to interact with plant hosts. Collectively, our findings expand the transcriptome resources and provide valuable insights into the gene networks involved in conidial germination and initiation of infection in pathogenic versus endophytic fungus.
2024-11-05 | GSE277627 | GEO
Project description:Conidial germination marks the beginning of the fungal life cycle, and understanding the genes associated with conidial germination provides insights into fungal pathogenicity and host interactions. Here, we use comparative transcriptomics to demonstrate the transcriptional similarities and differences during conidial germination and initial colony establishment in a plant pathogenic and an endophytic fungus, Fusarium graminearum and M. anisopliae, respectively. We compared the transcriptomes of F. graminearum and M. anisopliae across four stages of conidial germination: fresh conidia, polar growth, hyphal extension, and either first hyphal branching (on medium) or appressorium formation (on barley). F. graminearum exhibited a higher upregulation of CAZyme, specialized metabolite and effector genes compared to M. anisopliae during interaction with the host, particularly in the appressorium stage, reflecting its pathogenic nature. The appressorium structures formed when M. anisopliae conidia germinated on the host. The transcriptome analysis revealed that the fungus produced reduced transcript levels of CAZyme and specialized metabolite genes reflecting a less aggressive host penetration approach. The candidate genes associated with IAA synthesis were upregulated in M. anisopliae during the appressorium stage, supporting its endophytic lifestyle and suggests that the fungus uses a phytohormone based strategy to interact with plant hosts. Collectively, our findings expand the transcriptome resources and provide valuable insights into the gene networks involved in conidial germination and initiation of infection in pathogenic versus endophytic fungus.
2024-11-05 | GSE277787 | GEO
Project description:In opportunistic human pathogenic fungi, changes in gene expression play a crucial role in the evolution of growth stages from early spore germination through host infection. Comparative transcriptomics from diverse fungal pathogens along closely related non-pathogenic model provided insights of regulatory mechanisms behind the initiation of infectious processes by different fungi. We examined the gene expression patterns of 3,845 single-copy orthologous genes (SCOGs) across five phylogenetically distinct species, including the opportunistic human pathogens Fusarium oxysporum, Aspergillus fumigatus, and A. nidulans, and nonpathogenic species Neurospora crassa and Trichoderma asperelloides, at four sequential stages spore germination.
2024-12-31 | GSE279549 | GEO
Project description:Xylem sap proteome studies on susceptible or resistant tomato (Solanum lycopersicum) inoculated with endophytic and/or pathogenic strains of Fusarium oxysporum f.sp. lycopersici were conducted to get insights into the molecular differences between endophyte- and R-gene-mediated resistance (EMR and RMR). The EMR and RMR proteomes were compared to each other and to the mock control. Interestingly, specific PR-5 isoforms were found to exclusively accumulate during endophyte or genetic resistance, providing excellent markers to distinguish both resistance types at the molecular level.
2019-11-14 | PXD011072 | Pride
Project description:Fusarium fujikuroi is a biotechnologically important fungus due to its almost unique ability to produce gibberellic acids (GAs), a family of phytohormones. The fungus was described about 100 years ago as the causative agent of Bakanae (M-bM-^@M-^\foolish seedlingM-bM-^@M-^]) disease of rice. Apart from GAs, the fungus is known to produce pigments and mycotoxins, but the biosynthetic genes are known for only eight products. Here we present a high-quality genome sequence of the first member of the Gibberella fujikuroi species complex (GFC) that allowed de novo genome assembly with 12 scaffolds corresponding to the 12 chromosomes. In this work we focused on identification of all potential secondary metabolism-related gene clusters and their regulation in response to nitrogen availability by transcriptome, proteome, HPLC-FTMS and ChIP-seq analyses. We show that most of the cluster genes are regulated in a nitrogen-dependent manner, and that expression profiles fit to proteome and ChIP-seq data for some but not all clusters. Comparison with genomes of all available Fusarium species, including the recently sequenced F. mangiferae and F. circinatum, showed only a small number of common gene clusters and provides new insights into the divergence of secondary metabolism in the genus Fusarium. Phylogenetic analyses suggest that some gene clusters were acquired by horizontal gene transfer, while others were present in ancient Fusarim species and have evolved differently by gene duplications and losses. One polyketide synthase (PKS) and one non-ribosomal peptide synthetase (NRPS) gene cluster are unique for F. fujikuroi. Their products were identified by combining overexpression of cluster genes with HPLC-FTMS-based analyses. In planta expression studies suggest a specific role of the PKS19 product in rice infection. Our results indicate that comparative genomics together with the used genome-wide experimental approaches is a powerful tool to uncover new secondary metabolites and to understand their regulation at the transcriptional, translational and epigenetic levels. Examination of 3 different histone modifications, with 2 growth conditions for one of the modifications (Total of 4 samples)
2013-10-16 | E-GEOD-46033 | biostudies-arrayexpress
Project description:Annotation of small RNAs from 11 Drosophila species for the purpose of non-coding RNA annotation and comparative genomics assessment.
2017-11-20 | GSE98013 | GEO