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:Durum wheat (Triticum turgidum L. ssp. durum) is a major cereal and staple in the semi-arid regions of the Mediterranean Basin. After assembling the Platinum-quality reference genome for Svevo durum wheat cultivar, coupling PACBIO HiFi long read 35X sequencing with BIONANO Optical Mapping and Hi-C conformation capture, a complete and accurate gene annotation was then obtained by coupling Illumina RNASeq and Nanopore Isoseq sequencing from multiple tissues. The gene expression was investigated in root and shoot samples collected from plants grown under control condition or subjected to heat, salinity and osmotic stresses or to nitrogen application to create a transcriptional atlas of durum wheat response to abiotic stresses.
2026-07-29 | GSE318338 | 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:Durum wheat (Triticum turgidum L. ssp. durum) is a major cereal and staple in the semi-arid regions of the Mediterranean Basin. It originates from BBAA wild tetraploid domesticated in Neolithic era, later evolving to domesticated emmer and then to up to 11 T. turgidum subspecies, including durum wheat landraces and modern cultivars. Tetraploid wheat is the donor of the A and B genomes of hexaploid bread wheat (DDAABB), representing therefore a valuable source of genetic variability and beneficial alleles for both durum and bread wheat breeding. After assembling the Platinum-quality reference genome for Svevo durum wheat cultivar coupling PACBIO HiFi long read 35X sequencing with BIONANO Optical Mapping and Hi-C conformation capture, a complete and accurate gene annotation was then obtained by coupling Illumina RNASeq and Nanopore Isoseq sequencing from multiple tissues. The expression of 68,154 high confidence genes together with more than 100,000 low confidence, TE-related or long non-coding genes was investigated on 30 diverse tissues from grain, root, leaf, and spike samples across multiple developmental time points to create a transcriptional atlas of durum wheat development.
2026-07-29 | GSE318160 | 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-carbo
| PXD041703 |
Project description:Transcriptional regulation of durum wheat response to abiotic stress
| PRJNA1418604 | ENA