Multi-omics atlas of combinatorial abiotic stress responses in wheat
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ABSTRACT:
PROVIDER: PRJNA758708 | ENA |
REPOSITORIES: ENA
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Project description:We present a transcriptomic atlas of abiotic stress tolerance in wheat. We employed a systems biology approach to study physiological, metabolomic and transcriptomic responses associated with heat, drought, salinity and their possible combinations. Our objectives were to (1) rank stress treatments based on the overall physiological and growth impacts, (2) identify the core sets of genes common to a particular stress type, (3) examine pathways that are uniquely expressed in the various stress combinations, (4) detect associations between phenotypic and transcriptomic responses, (5) suggest possible transcription factors for further characterization and use in improving wheat performance in multi-stress environments.
2023-06-02 | GSE183007 | GEO
Project description:Integration of multi-omics data can provide information on biomolecules from different layers to illustrate the complex biology systematically. Here, we built the first global quantitative atlas containing transcriptomes, proteomes, phospho-proteomes and acetyl-proteomes of 20 tissues in common wheat. We identified 132,570 transcripts, 32,256 proteins, 69,364 phosphorylation sites, and 34,974 acetylation sites across wheat development stages. Our data demonstrated that homoeolog expression bias exists divergence at different omics layers. Regulatory networks dissected critical proteins or genes controlling important biology processes. Four wheat trait-gene families refer to timely flowering, disease resistance, starch biosynthesis-related genes, and seed storage proteins were used as examples to verify our data and shed novel inlight on the importance of post-translational modifications in wheat previously unknown. Importantly, a novel Fusarium crown rot (FCR) resistant gene delta-1-pyrroline-5-carboxylate synthase (TaP5CS1) was identified by FCR-responsive multi-omics techniques. We found that TaP5CS1 confers FCR tolerance via increased proline content and is regulated by histone deacetylase 9 (TaHDA9). Our multi-omics atlas data will accelerate function and mechanism studies of important traits in wheat.
2023-05-25 | PXD042492 |
Project description:The yield of wheat is highly impacted by environmental stresses. The combinatorial regulation of sequence-specific transcription factors(TFs) defines a regulatory network that underlies plant stress responses. Here we created a comprehensive catalog of genomic binding sites of 115 TFs underlying abiotic stress responses by leveraging DAP-seq in Triticum Urartu, along with epigenomic profiles. The majority of gene distant TF binding sites(TFBS) are embedded in transposable elements(TEs), whose functional relevance was supported by a signature of purifying selection and active epigenomic features. Furthermore, ~30% non-TE TFBS share high sequence similarity with TE-embeded TFBS, potentially derived from Triticeae-specific TEs and have almost no sequence homology in non-Triticeae species. The expansion of TE-derived TFBS in wheat linked to wheat-specific stress responsive genes, suggesting that TEs are an important driving force for regulatory innovation. Altogether, TEs have significantly and continuously shaped regulatory network in wheat adaptation.
2021-08-31 | GSE167228 | GEO
Project description:The yield of wheat is highly impacted by environmental stresses. The combinatorial regulation of sequence-specific transcription factors(TFs) defines a regulatory network that underlies plant stress responses. Here we created a comprehensive catalog of genomic binding sites of 115 TFs underlying abiotic stress responses by leveraging DAP-seq in Triticum Urartu, along with epigenomic profiles. The majority of gene distant TF binding sites(TFBS) are embedded in transposable elements(TEs), whose functional relevance was supported by a signature of purifying selection and active epigenomic features. Furthermore, ~30% non-TE TFBS share high sequence similarity with TE-embeded TFBS, potentially derived from Triticeae-specific TEs and have almost no sequence homology in non-Triticeae species. The expansion of TE-derived TFBS in wheat linked to wheat-specific stress responsive genes, suggesting that TEs are an important driving force for regulatory innovation. Altogether, TEs have significantly and continuously shaped regulatory network in wheat adaptation.
2021-08-31 | GSE182693 | GEO
Project description:The yield of wheat is highly impacted by environmental stresses. The combinatorial regulation of sequence-specific transcription factors(TFs) defines a regulatory network that underlies plant stress responses. Here we created a comprehensive catalog of genomic binding sites of 115 TFs underlying abiotic stress responses by leveraging DAP-seq in Triticum Urartu, along with epigenomic profiles. The majority of gene distant TF binding sites(TFBS) are embedded in transposable elements(TEs), whose functional relevance was supported by a signature of purifying selection and active epigenomic features. Furthermore, ~30% non-TE TFBS share high sequence similarity with TE-embeded TFBS, potentially derived from Triticeae-specific TEs and have almost no sequence homology in non-Triticeae species. The expansion of TE-derived TFBS in wheat linked to wheat-specific stress responsive genes, suggesting that TEs are an important driving force for regulatory innovation. Altogether, TEs have significantly and continuously shaped regulatory network in wheat adaptation.
2021-08-31 | GSE167227 | GEO
Project description:In this study, we set to take advantage of Marchantias less complex signalling architecture to better understand how plants respond to environmental cues such as stress and time of the day, to modulate the expression of genes and biological pathways. To this end, we constructed an abiotic stress gene expression atlas of Marchantia comprising seven abiotic stresses (darkness, high light, cold, heat, nitrogen deficiency, salt, mannitol) and their pairwise combinations (e.g., cold + salt). We also measured gene expression at six timepoints of a day (12h light/ 12h darkness)
2021-11-17 | E-MTAB-11141 | biostudies-arrayexpress
Project description:Integration of multi-omics data can provide information on biomolecules from different layers to illustrate the complex biology systematically. Here, we built the first global quantitative atlas containing transcriptomes, proteomes, phospho-proteomes and acetyl-proteomes of 20 tissues in common wheat. We identified 132,570 transcripts, 32,256 proteins, 69,364 phosphorylation sites, and 34,974 acetylation sites across wheat development stages. Our data demonstrated that homoeolog expression bias exists divergence at different omics layers. Regulatory networks dissected critical proteins or genes controlling important biology processes. Four wheat trait-gene families refer to timely flowering, disease resistance, starch biosynthesis-related genes, and seed storage proteins were used as examples to verify our data and shed novel inlight on the importance of post-translational modifications in wheat previously unknown. Importantly, a novel Fusarium crown rot (FCR) resistant gene delta-1-pyrroline-5-carbo
2023-04-20 | PXD041703 |
Project description:Marchantia abiotic stress combination and diurnal gene expression atlas
| PRJEB48734 | ENA
Project description:Purpose: To identify abiotic stress responsive and tissue specific miRNAs at genome wide level in wheat (Triticum aestivum) Results: Small RNA libraries were constructed from four tissues (root, shoot, mature leaf and spikelets) and three stress treatments of wheat seedlings (control, high temperature, salinity and water-deficit). A total of 59.5 million reads were obtained by high throughput sequencing of eight wheat libraries, of which 32.5 million reads were found to be unique. Using UEA sRNA workbench we identified 47 conserved miRNAs belonging to 20 families, 1030 candidate novel and 51 true novel miRNAs. Several of these miRNAs displayed tissue specific expression whereas few were found to be responsive to abiotic stress treatments. Target genes were predicted for miRNAs identified in this study and their grouping into functional categories revealed that the putative targets were involved in diverse biological processes. RLM-RACE of predicted targets of three conserved miRNAs (miR156, miR160 and miR164) confirmed their mRNA cleavage, thus indicating their regulation at post-transcriptional level by corresponding miRNAs. Expression profiling of confirmed target genes of these miRNAs was also performed. Conclusions: This is the first comprehensive study on profiling of miRNAs in a variety of tissues and in response to several abiotic stresses in wheat. Our findings provide valuable resource for better understanding on the role of miRNAs in stress tolerance as well as plant development. Additionally, this information could be utilized for designing wheat plants for enhanced abiotic stress tolerance and higher productivity.
2014-08-20 | GSE53487 | 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