Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1082299 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Purpose: Identify differentially regulated genes in three Bacteroides species (B. intestinalis, B. cellulosylitycus, and B. oleiciplenus) under xylose:arabinose growth compared to insoluble wheat arabinoxylan Methods: Bacterial mRNA profiles of mid-log cultures were generated by deep sequencing using Illumina 4000, in duplicates. The sequences were trimmed based on quality scores using Trimmomatic.
2020-11-14 | GSE161471 | GEO
Project description:Despite the broad use of single-cell and single-nucleus RNA sequencing in plant research, accurate cluster annotation in less studied plant species remains a major challenge due to the lack of validated marker genes. Here, using soil-grown wheat roots as a model, we generated a single-cell RNA-sequencing (scRNA-seq) atlas and annotated cluster identities in an unbiased way by transferring existing annotations from publicly available datasets in wheat, rice, maize and Arabidopsis. These cross-species orthology-based predictions were next validated using untargeted spatial transcriptomics. This information refined existing cluster annotations for different datasets across key plant model species. We then used the validated clusters to generate cell type-specific gene regulatory networks for root tissues of wheat and two other monocot crop species. By integrating all available data, including homeolog expression in wheat, we predicted reliable tissue-specific markers which are conserved across different species. In summary, we provided an annotated and validated single cell transcriptomic resource for soil-grown wheat root apical meristems and revealed conserved cell type-specific regulators and markers across species. These data expand upon previous root single cell atlas resources in crops, and will facilitate cell type annotation in non-model plant species in the future.
2025-01-06 | GSE271725 | GEO
Project description:Despite the broad use of single-cell and single-nucleus RNA sequencing in plant research, accurate cluster annotation in less studied plant species remains a major challenge due to the lack of validated marker genes. Here, using soil-grown wheat roots as a model, we generated a single-cell RNA-sequencing (scRNA-seq) atlas and annotated cluster identities in an unbiased way by transferring existing annotations from publicly available datasets in wheat, rice, maize and Arabidopsis. These cross-species orthology-based predictions were next validated using untargeted spatial transcriptomics. This information refined existing cluster annotations for different datasets across key plant model species. We then used the validated clusters to generate cell type-specific gene regulatory networks for root tissues of wheat and two other monocot crop species. By integrating all available data, including homeolog expression in wheat, we predicted reliable tissue-specific markers which are conserved across different species. In summary, we provided an annotated and validated single cell transcriptomic resource for soil-grown wheat root apical meristems and revealed conserved cell type-specific regulators and markers across species. These data expand upon previous root single cell atlas resources in crops, and will facilitate cell type annotation in non-model plant species in the future.
2025-01-06 | GSE270342 | GEO
Project description:The small RNA transcriptomes of bread wheat (Triticum aestivum L.) and its emerging model (Brachypodium distachyon (L.) Beauv) were obtained by using deep sequencing technology. Small RNA compositions were analyzed in these two species. In addition to 70 conserved microRNAs (miRNA) from 25 families, 23 novel wheat miRNAs were identified. For Brachypodium, 12 putative miRNAs were predicted from a limited number of ESTs, of which one was a potential novel miRNA. Also, 94 conserved miRNAs from 28 families were identified in this species. Expression validation was performed for several novel wheat miRNAs. RNA ligase-mediated 5' RACE experiments demonstrated their capability to cleave predicted target genes including three disease resistant gene analogs. Differential expression of miRNAs was observed between Brachypodium vegetative and reproductive tissues, suggesting their different roles at the two growth stages. Our work significantly increases the novel miRNA numbers in wheat and provides the first set of small RNAs in Brachypodium distachyon. Keywords: Small RNA
2009-06-08 | GSE16177 | GEO
Project description:To reveal the origin of the wheat B sub-genome, we performed the whole genome sequencing of sitopsis species. Besides, we also conducted the RNA seq of Ae.speltoides and hexaploid wheat Chinese Spring.
2023-08-22 | GSE197464 | GEO
Project description:To reveal the origin of the wheat B sub-genome, we performed the whole genome sequencing of sitopsis species. Besides, we also conducted the RNA seq of Ae.speltoides and hexaploid wheat Chinese Spring.
2023-08-22 | GSE197048 | GEO
Project description:Fusarium Head Blight (FHB) is a disease of wheat and other cereal crops, where Fusarium graminearum and related species infects the wheat inflorescence during and post-anthesis. The fungus produces trichothecene toxins that accumulate in the grain of infected head, and are required for disease spread. Microarrays were used to observe differential gene expression in the uninoculated spikelets of FHB-challenged wheat spikes in three wheat genotypes. A summary of our findings will be published in Plant Pathology.
2011-09-01 | GSE28973 | GEO
Project description:Phenotypic responses to biotic stresses are often studied as the interactions between two species; however, in the phytobiome, these responses frequently result from complex interactions involving several organisms. Here, we show that variation in chlorosis caused by Russian wheat aphid (Diuraphis noxia) feeding is determined, in part, by aphid-associated bacteria. Proteomic analysis of fluids injected into a sterile medium by the aphid during feeding indicate that 99% of the proteins are of bacterial origin. Of these, the greatest proportion are produced by bacteria in the order Enterobacteriales. Bacteria from five genera in four families that have the capacity to produce these proteins were isolated directly from aphids as well as from wheat leaves only after D. noxia feeding. By themselves or in combination, these bacteria were not virulent to wheat, even at high inoculum levels. Metagenomic analysis showed that the same five D. noxia-associated genera dominated the non-Buchnera component of the aphid microbiome, and that representation of these genera was reduced in aphids from colonies established after isolation of newborn nymphs from their mothers prior to feeding (‘isolated’ aphids). Isolation or treatment with antibiotics reduced bacterial numbers, and these aphids caused less feeding damage on wheat than non-isolated or non-antibiotic treated aphids. Our data show that bacterial proteins are a significant component of Russian wheat aphid saliva, that the bacteria producing these proteins are associated with aphids and plants fed upon by aphids, and that these aphid-associated bacteria facilitate aphid virulence to wheat.
2020-11-09 | PXD010663 | Pride
Project description:The aim for this study was to compare the differences in the methylome of three Russian wheat aphid populations that differ in virulence and bacterial load. Differences in the methylome of US Russian wheat aphid biotype 2 (US-RWA2) that have undergone removal of their phytobiomes through isolation of newly born nymphs from their mothers compared to nymphs who stayed in close proximity to their progenitors. US-RWA1 is the least virulent biotype and US-RWA2 is the most virulent biotype. The isolated US-RWA2 population (with a reduced bacterial load) has been shown to be less virulent than the co-fed population (Luna et al., 2018). The corresponding two methylomes were then compared to the methylome of US Russian wheat aphid biotype 1 (US-RWA1 is less virulent than US-RWA2) to ascertain the contribution (or lack thereof) of the phytobiome in regards to the increased/decreased virulence of phytobiome present and absent aphids. We investigated the overall, genic, intergenic, exonic and intronic methylation - as well as genic and intergenic hemimethylation -all three available contexts ( CpG, CHG and CHH) through use of the Bismark pipeline. These findings were used to ascertain to what effect the phytobiome (bacterial load) had on methylation within the US Russian wheat aphid biotypes.
2022-06-30 | GSE185975 | GEO