Comparative transcriptomics analyses of fruiting body development in Fusarium species
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PROVIDER: PRJNA512482 | ENA |
REPOSITORIES: ENA
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Project description:Fusarium neocosmosporiellum (formerly Neocosmospora vasinfecta) has been reported as a fruit- and root-rot pathogen of numerous field crops, although it is not known to cause significant losses on any crop. This cosmopolitan species has also been reported as an opportunistic human pathogen, from infected soybean cyst nematodes, deer dung, and soil, and it possesses a highly active CO2 fixation mechanism. To better understand the metabolic potential of this fungus, we sequenced the genome of one isolate of F. neocosmosporiellum and compared its gene content with previously published Fusarium genomes. The predicted gene numbers were similar to F. graminearum, but the F. neocosmosporiellum genome contained more carbohydrate metabolism-related and transmembrane transport genes, and it appears to have a greater ability to utilize resources in the environment as a cosmopolitan saprotroph. Transcriptome data during perithecium development was compared with that of the model plant pathogen F. graminearum. The F. neocosmosporiellum genome included both MAT1-1 and MAT1-2 idiomorphs, as in the homothallic F. graminearum, however MAT gene organization and their expression patterns during perithecium development differed in these species. We also found that many transmembrane transport genes were differentially expressed during perithecium development, which may account for the larger perithecia of F. neocosmosporiellum. Finally, comparative analysis of the secondary metabolite gene clusters identified several polyketide synthase genes that were induced during perithecium development. Deletion of a novel polyketide synthase gene in F. neocosmosporiellum resulted in a defective perithecium phenotype. In summary, comparative analysis of the transcriptional programs during perithecium development has provided novel insights into morphological and physiological diversification in F. neocosmosporiellum.
2019-06-20 | GSE124553 | GEO
Project description:Fusarium graminearum and F. verticillioides are devastating cereal pathogens with very different life history and ecological characteristics. F. graminearum is homothallic, and sexual spores are an important component of its life cycle, responsible for disease initiation. F. verticilloides is heterothallic, and produces only modest numbers of fruiting bodies, which are not a significant source of inoculum. To identify corresponding differences in the transcriptional program underlying fruiting body development in the two species, comparative expression was performed, analyzing six developmental stages. To accompany the transcriptional analysis, detailed morphological characterization of F. verticillioides development was performed and compared to a previous morphological analysis of F. graminearum. Morphological development was similar between the two species, except for the observation of possible trichogynes in F. verticillioides ascogonia, which have not been previously reported for any Fusarium species. Expression of over 9000 orthologous genes were measured for the two species. Functional assignments of highly expressed orthologous genes at each time-point revealed the majority of highly expressed genes fell into the M-bM-^@M-^XM-bM-^@M-^Xunclassified proteinsM-bM-^@M-^YM-bM-^@M-^Y category, reflecting the lack of characterization of genes for sexual development in both species. Simultaneous examination of morphological development and stage-specific gene expression suggests that degeneration of the paraphyses during sexual development is an apoptotic process. Expression of mating type genes in the two species differed, possibly reflecting the divergent roles they play in sexual development. Overall, the differences in gene expression reflect the greater role of fruiting bodies in the life cycle and ecology of F. graminearum versus F. verticillioides. mRNA were sampled and compared from six time points across sexual reproduction in two Fusarium species
2014-09-30 | E-GEOD-61865 | biostudies-arrayexpress
Project description:Fusarium graminearum and F. verticillioides are devastating cereal pathogens with very different life history and ecological characteristics. F. graminearum is homothallic, and sexual spores are an important component of its life cycle, responsible for disease initiation. F. verticilloides is heterothallic, and produces only modest numbers of fruiting bodies, which are not a significant source of inoculum. To identify corresponding differences in the transcriptional program underlying fruiting body development in the two species, comparative expression was performed, analyzing six developmental stages. To accompany the transcriptional analysis, detailed morphological characterization of F. verticillioides development was performed and compared to a previous morphological analysis of F. graminearum. Morphological development was similar between the two species, except for the observation of possible trichogynes in F. verticillioides ascogonia, which have not been previously reported for any Fusarium species. Expression of over 9000 orthologous genes were measured for the two species. Functional assignments of highly expressed orthologous genes at each time-point revealed the majority of highly expressed genes fell into the ‘‘unclassified proteins’’ category, reflecting the lack of characterization of genes for sexual development in both species. Simultaneous examination of morphological development and stage-specific gene expression suggests that degeneration of the paraphyses during sexual development is an apoptotic process. Expression of mating type genes in the two species differed, possibly reflecting the divergent roles they play in sexual development. Overall, the differences in gene expression reflect the greater role of fruiting bodies in the life cycle and ecology of F. graminearum versus F. verticillioides.
2014-09-30 | GSE61865 | GEO
Project description:Transcriptome analyses during fruiting body formation in Fusarium graminearum and Fusarium verticillioides reflect species life history and ecology
| PRJNA262571 | ENA
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.
2019-06-18 | GSE132826 | GEO
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.
2014-12-19 | E-GEOD-43297 | biostudies-arrayexpress
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.
2024-01-26 | GSE245082 | GEO
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.
2019-04-19 | GSE123178 | GEO
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.
2014-12-19 | GSE43297 | GEO
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. 5'-SAGE analysis of the transcriptomes of vegetative mycelium and primordium of C. cinerea by 454 GS20 high-throughput pyrosequencer
2013-01-10 | E-GEOD-40722 | biostudies-arrayexpress