Ontology highlight
ABSTRACT:
PROVIDER: PRJNA754593 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR15459100_1.fastq.gz | Fastqsanger.gz | |||
| SRR15459100_2.fastq.gz | Fastqsanger.gz | |||
| SRR15459101_1.fastq.gz | Fastqsanger.gz | |||
| SRR15459101_2.fastq.gz | Fastqsanger.gz | |||
| SRR15459102_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 320 |
Similar Datasets
Project description:Wood-degrading fungi play a critical role in global carbon cycling, and their varied mechanisms for deconstruction offer pathways for industrial bioconversion. In this study, we used comparative genomics to isolate upregulation patterns among fungi with brown rot (carbohydrate-selective) or white rot (lignin-degrading) nutritional modes. Specifically, we used whole-transcriptome profiling to compare early, middle, and late decay stages on wood wafers, matching differentially-expressed gene (DEG) patterns with fungal growth and enzyme activities. This approach highlighted 34 genes uniquely upregulated in early brown rot stages, with notable candidates involved in generating reactive oxygen species (ROS) as a pretreatment mechanism during brown rot. This approach further isolated 18 genes in late brown rot stages that may be adapted to handle oxidatively-reacted lignocellulose components. By summing gene expression levels in functional classes, we also identified a broad and reliable distinction in glycoside hydrolase (GH) versus lignocellulose oxidative (LOX) transcript counts that may reflect the energy investment burden of lignin-degrading machinery among white rot fungi.
2018-01-05 | GSE108189 | GEO
Project description:Brown rot fungi evolved the unique strategy to efficiently decay wood structures and selectively extract carbohydrates, and this involved the sophistical regulation of functional genes (Zhang et al., PNAS, 2016, 113: 10968-). However, the regulatory mechanisms of brown rot genes were not well known, impeding the implication and application of brown rot machinery in biomass conversions. In this work, we systematically studied the roles of environmental carbon signals (e.g., aspen, cellobiose, glucose and no-carbon) in regulating gene expression in model brown rot fungus Postia placenta by RNA-seq. We found the complex substrate aspen (Populus sp.), but not the commonly recognized disaccharide cellobiose, was the universal inducer for Carbohydrate Active Enzymes (CAZYs) expression. Even though, cellobiose clearly induced the expression of cellulase (GH5 and GH12, endoglucanase) and xylanase (GH10, endoxylanase) (cellobiose vs. no-carbon, fold change > 4), as we reported previously (Zhang and Schilling, FGB, 2017, 106: 1-). When response to easy to use carbons, P. placenta lost the CCR effect on the main-chain cleaving CAZYs expression, but kept this repressing effect on side-chain cleaving CAZYs and AAs, which indicated a clear adaption relative to that in saprotrophic ascomycete ancestors. This “loss of CCR effect” was independent of the glucose concentrations. To explore the distinctive brown rot regulatory machinery, the gene modules subjected to inducing or CCR effects were then used to predict the regulatory motifs and transcriptional factors to build the regulatory network in P. placenta. Together, these findings will facilitate us to understand the adaptions of regulatory elements in brown rot fungi, as well as the efficient brown rot strategy.
2018-09-11 | GSE119714 | GEO
Project description:Brown rot fungi have great potential in biorefinery wood conversion systems, because they are the primary wood decomposers in coniferous forests and have an efficient lignocellulose degrading system. Their initial wood degradation mechanism is thought to consist of an oxidative radical-based system that acts sequentially with an enzymatic saccharification system, but the complete molecular mechanism of this system has not yet been elucidated. Some studies have shown that wood degradation mechanisms of brown rot fungi have diversity in their substrate selectivity. Gloeophyllum trabeum, one of the most studied brown rot species, has broad substrate selectivity and even can degrade some grasses. However, the basis for this broad substrate specificity is poorly understood. In this study, we performed RNA-seq analyses on G. trabeum grown on media containing glucose, cellulose, or Japanese cedar (Cryptomeria japonica) as the sole carbon source. Beyond the gene expression on glucose, 1129 genes were upregulated on cellulose and 1516 genes were upregulated on cedar. Carbohydrate Active enZyme (CAZyme) genes upregulated on cellulose and cedar media by G. trabeum included GH12, GH131, CE1, AA3_1, AA3_2, AA3_4 and AA9, which is a newly reported expression pattern for brown rot fungi. The upregulation of both terpene synthase and cytochrome P450 genes on cedar media suggests the potential importance of these genes in the production of secondary metabolites associated with the chelator-mediated Fenton reaction. These results provide new insights into the inherent wood degradation mechanism of G. trabeum and the diversity of brown rot mechanisms.
2020-08-05 | GSE155681 | GEO
Project description:Transcriptome analysis was performed on the rhizome tissues of Atractylodes macrocephala under different treatments. The four treatments were: sterile water irrigation alone, FS root irrigation, FS and AM201 root irrigation, and FS combined with methyltobuzin (TM) root irrigation. And the differential genes between AM201 and FO groups were identified and compared, which helps to reveal the resistance mechanism of AM201 to Atractylodes macrocephala root rot disease
2024-01-30 | GSE254183 | GEO
Project description:The response mechanisms, recognition and specificity of conifer trees during interaction with pathogenic, saprotrophic or symbiotic ectomycorrhizal fungus were investigated. The roots of Pinus sylvestris were challenged for fifteen days with either Heterobasidion annosum (a pathogenic root rot fungus which attacks Norway spruce, Scots pine and broad leaf trees); Laccaria bicolor (an obligate ectomycorrhizal symbiont); or Trichoderma aureoviride (an obligate saprotroph). The gene expression data from cDNA micro-arrays consisting of 2176 Pinus taeda genes were analysed using 2-interconnected mixed linear model statistical approach. The result of the pairwise comparisons of the different treatments against un-inoculated control led to identification of genes specifically differentially expressed in the pathogenic, saprotrophic and symbiotic interactions. The results were compared with similar data obtained for two other interaction stages: 1 and 5 days post inoculation. The result of this comprehensive expression profiling will hopefully shed more light on the mechanistic basis for recognition and response of conifer trees to pathogenic and non-pathogenic fungi. Keywords: stress response
2006-07-31 | GSE5407 | GEO
Project description:The response mechanisms, recognition and specificity of conifer trees during interaction with pathogenic, saprotrophic or symbiotic ectomycorrhizal fungus were investigated. The roots of Pinus sylvestris were challenged for five days with either Heterobasidion annosum (a pathogenic root rot fungus which attacks Norway spruce, Scots pine and broad leaf trees); Laccaria bicolor (an obligate ectomycorrhizal symbiont); or Trichoderma aureoviride (an obligate saprotroph). The gene expression data from cDNA micro-arrays consisting of 2176 Pinus taeda genes were analysed using 2-interconnected mixed linear model statistical approach. The result of the pairwise comparisons of the different treatments against un-inoculated control led to identification of genes specifically differentially expressed in the pathogenic, saprotrophic and symbiotic interactions. The results were compared with similar data obtained for two other interaction stages: 1 and 15 days post inoculation. The result of this comprehensive expression profiling will hopefully shed more light on the mechanistic basis for recognition and response of conifer trees to pathogenic and non-pathogenic fungi. Keywords: stress response
2006-07-31 | GSE5408 | GEO
Project description:Plant response to insect feeding appears to be highly specific with regard to the organisms in the system. Here, we report on the interaction between grapevine Vitis vinifera plants and a phloem-feeding insect pest, the vine mealybug Planococcus ficus. Plants were exposed to P. ficus for periods of 6 hours and 96 hours, after which they were analysed for gene expression levels using microarrays and quantitative real-time PCR (qPCR). Both methods showed that grapevine displayed only a minimal response to mealybug feeding at the transcript level at both time periods. Intermediate grapevine exposure times (24, 48 and 72 hours) to P. ficus feeding were investigated using qPCR analysis of ten additional genes associated with known plant defense responses. Results showed that only a single gene, pathogenesis-related protein 1, was differentially expressed after 48 hours of mealybug feeding. During the course of mealybug feeding, however, a number of other genes were significantly up- or down-regulated at certain time points. Thus, it appears as if grapevine responds minimally to feeding by P. ficus as well as within a very narrow time period. The relative lack of grapevine plant defense mechanisms may be a result of the feeding strategies of mealybugs.
2012-12-01 | GSE32343 | GEO
Project description:Phytophthora parasitica is one of the most widespread Phytophthora species, which is known to cause root rot, foot rot/gummosis and brown rot of fruits in citrus. In this study, we have analyzed the transcriptome of a commonly used citrus rootstock Carrizo citrange in response to P. parasitica infection using the RNA-seq technology. In total, we have identified 6692 differentially expressed transcripts (DETs) among P. parasitica-inoculated and mock-treated roots. Of these, 3960 genes were differentially expressed at 24 hours post inoculation and 5521 genes were differentially expressed at 48 hours post inoculation. Gene ontology analysis of DETs suggested substantial transcriptional reprogramming of diverse cellular processes particularly the biotic stress response pathways in Carrizo citrange roots. Many R genes, transcription factors, and several other genes putatively involved in plant immunity were differentially modulated in citrus roots in response to P. parasitica infection. Analysis reported here lays out a strong foundation for future studies aimed at improving resistance of citrus rootstocks to P. parasitica.
2019-04-13 | GSE129758 | GEO
Project description:Wood-degrading brown rot fungi are essential recyclers of plant biomass in forest ecosystems. Their efficient cellulolytic systems, which have potential biotechnological applications, apparently depend on a combination of two mechanisms: lignocellulose oxidation by reactive oxygen species (ROS) and polysaccharide hydrolysis by a limited set of glycoside hydrolases (GHs). Given that ROS are strongly oxidizing and non-selective, these two steps are likely segregated. A common hypothesis has been that brown rot fungi use a concentration gradient of chelated metal ions to confine ROS generation inside wood cell walls before enzymes can infiltrate. We examined an alternative: that lignocellulose-oxidation (LOX) components involved in ROS production are differentially expressed by brown rot fungi ahead of GH components. We used spatial mapping to resolve a temporal sequence in Postia placenta, sectioning thin wood wafers colonized directionally. Among sections, we measured gene expression by whole transcriptome sequencing (RNAseq) and assayed relevant enzyme activities. We found a marked pattern of LOX upregulation in a narrow (5-mm; 48-hr) zone at the hyphal front, which included many genes likely involved in ROS generation. Upregulation of GH5 endoglucanases and many other GHs clearly occurred later, behind the hyphal front, with notable exceptions of two likely expansins and a GH28 pectinase. Our results support a staggered mechanism for brown rot that is controlled by differential expression rather than microenvironmental gradients. This mechanism likely results in an oxidative pretreatment of lignocellulose, possibly facilitated by expansin- and pectinase-assisted cell wall swelling, before cellulases and hemicellulases are deployed for polysaccharide depolymerization. We sequenced mRNA from 9 Postia placenta samples taken from 3 wood sections of wafer design, with 3 bioreplicates for each wood section, to compare the gene expression during brown rot processes. Three wood sections of the wafer are representing early to late decay stages.
2016-07-18 | E-GEOD-84529 | biostudies-arrayexpress
Project description:Characterization of secretome of two white rot and two brown rot fungal species grown on aspen. Goal is to utilize temporal sampling to assist in elucidating lignocellulose degradation mechanism
2018-07-16 | PXD009480 | Pride