Triticeae
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA272886 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1915961_1.fastq.gz | Fastqsanger.gz | |||
| SRR1915961_2.fastq.gz | Fastqsanger.gz | |||
| SRR1915952_1.fastq.gz | Fastqsanger.gz | |||
| SRR1915952_2.fastq.gz | Fastqsanger.gz | |||
| SRR1915962_1.fastq.gz | Fastqsanger.gz |
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Project description:Despite their importance, there remains to be few large scale expression-based studies of tissue-specific expression information in the species belonging to the Triticeae. We used the 55K Affymetrix GeneChip® Wheat Genome Array to generate a gene expression atlas of triticale tissues. The global transcriptional profiles of seed tissues (embryo, endosperm, crease, pericarp and epiderm) and vegetative tissues (root, coleoptile, stem and leaf) were analyzed and co-regulated as well as preferentially expressed genes were identified. Data analysis revealed both novel and conserved regulatory factors underlying Triticeae tissue development and function.
2014-12-24 | GSE43127 | GEO
Project description:Cereal genomes have undergone repeated polyploidization and transposable element (TE) proliferation, collectively generating complex regulatory landscapes. The evolutionary trajectories and functional implications of these landscapes, however, remain largely unexplored. By employing chromatin-bound RNA sequencing across seven cereal species, we systematically mapped 45,952 regulatory element transcripts (RETs), including 32,867 distal RETs corresponding to enhancer RNAs (eRNAs). Our analysis reveals that 56% of lineage-specific eRNAs originate from TE expansions, suggesting TEs as significant reservoirs of species-specific regulatory innovation in cereals. Notably, we uncovered a remarkable similarity in defense-related function, root-specific expression, and TE-derived origin of eRNAs across ancient and recent evolutionary layers of Triticeae, suggesting recurrent recruitment of TE-derived root-associated regulatory elements during Triticeae evolution. Furthermore, we found that young eRNA pairs in hexaploid wheat with high sequence similarity, many originating from RLG_famc8.3 and DTC_famc4.3, exhibit pronounced root specificity and coordinated expression, suggesting a targeted amplification and refinement of the successful ancestral regulatory strategy established after Triticeae divergence. To facilitate community access, we developed Cereal-eRNAdb (http://bioinfo.cemps.ac.cn/Cereal-eRNAdb/), a comprehensive database integrating 69,426 eRNAs with functional annotations across 296 samples. Our work indicates that TE-mediated innovation of root-specific eRNAs as a candidate mechanism that may contribute to Triticeae adaptation and provides a foundational resource for exploiting regulatory variation in cereal crop breeding.
2026-06-22 | GSE284459 | GEO
Project description:Cereal genomes have undergone repeated polyploidization and transposable element (TE) proliferation, collectively generating complex regulatory landscapes. The evolutionary trajectories and functional implications of these landscapes, however, remain largely unexplored. By employing chromatin-bound RNA sequencing across seven cereal species, we systematically mapped 45,952 regulatory element transcripts (RETs), including 32,867 distal RETs corresponding to enhancer RNAs (eRNAs). Our analysis reveals that 56% of lineage-specific eRNAs originate from TE expansions, suggesting TEs as significant reservoirs of species-specific regulatory innovation in cereals. Notably, we uncovered a remarkable similarity in defense-related function, root-specific expression, and TE-derived origin of eRNAs across ancient and recent evolutionary layers of Triticeae, suggesting recurrent recruitment of TE-derived root-associated regulatory elements during Triticeae evolution. Furthermore, we found that young eRNA pairs in hexaploid wheat with high sequence similarity, many originating from RLG_famc8.3 and DTC_famc4.3, exhibit pronounced root specificity and coordinated expression, suggesting a targeted amplification and refinement of the successful ancestral regulatory strategy established after Triticeae divergence. To facilitate community access, we developed Cereal-eRNAdb (http://bioinfo.cemps.ac.cn/Cereal-eRNAdb/), a comprehensive database integrating 69,426 eRNAs with functional annotations across 296 samples. Our work indicates that TE-mediated innovation of root-specific eRNAs as a candidate mechanism that may contribute to Triticeae adaptation and provides a foundational resource for exploiting regulatory variation in cereal crop breeding.
2026-06-22 | GSE284460 | GEO
Project description:Despite their importance, there remains a paucity of large scale expression-based studies of reproductive development in the species belonging to the Triticeae. As a first step to address this deficiency, a gene expression atlas of triticale reproductive development was generated using the 55K Affymetrix GeneChip® Wheat Genome Array. The global transcriptional profiles of the anther/pollen, ovary and stigma were analyzed at concurrent developmental stages and co-regulated as well as preferentially expressed genes were identified. Data analysis revealed both novel and conserved regulatory factors underlying Triticeae floral development and function.
2012-11-01 | GSE41984 | GEO
Project description:Triticeae crops are major contributors to global food production and ensuring their capacity to reproduce and generate seeds is critical. However, despite their importance our knowledge of the proteins underlying Triticeae reproduction is severely lacking and this is not only true of pollen and stigma development, but also of their pivotal interaction. When the pollen grain and stigma are brought together they have each accumulated the proteins required for their intended meeting and accordingly studying their mature proteomes is bound to reveal proteins involved in their diverse and complex interactions. Using triticale as a Triticeae representative, gel-free shotgun proteomics was used to identify 11533 and 2977 mature stigma and pollen proteins respectively. These datasets, by far the largest to date, provide unprecedented insights into the proteins participating in Triticeae pollen and stigma development and interactions. The study of the Triticeae stigma has been particularly neglected and to begin filling this knowledge gap, a developmental iTRAQ analysis was performed revealing 647 proteins displaying differential abundance as the stigma matures in preparation for pollination. An in-depth comparison to an equivalent Brassicaceae analysis divulged both conservation and diversification in the makeup and function of proteins involved in the pollen and stigma encounter.
2023-03-08 | PXD038905 | Pride
Project description:Cereal genomes have undergone repeated polyploidization and transposable element (TE) proliferation, collectively generating complex regulatory landscapes. The evolutionary trajectories and functional implications of these landscapes, however, remain largely unexplored. By employing chromatin-bound RNA sequencing across seven cereal species, we systematically mapped 45,952 regulatory element transcripts (RETs), including 32,867 distal RETs corresponding to enhancer RNAs (eRNAs). Our analysis reveals that 56% of lineage-specific eRNAs originate from TE expansions, suggesting TEs as significant reservoirs of species-specific regulatory innovation in cereals. Notably, we uncovered a remarkable similarity in defense-related function, root-specific expression, and TE-derived origin of eRNAs across ancient and recent evolutionary layers of Triticeae, suggesting recurrent recruitment of TE-derived root-associated regulatory elements during Triticeae evolution. Furthermore, we found that young eRNA pairs in hexaploid wheat with high sequence similarity, many originating from RLG_famc8.3 and DTC_famc4.3, exhibit pronounced root specificity and coordinated expression, suggesting a targeted amplification and refinement of the successful ancestral regulatory strategy established after Triticeae divergence. To facilitate community access, we developed Cereal-eRNAdb (http://bioinfo.cemps.ac.cn/Cereal-eRNAdb/), a comprehensive database integrating 69,426 eRNAs with functional annotations across 296 samples. Our work indicates that TE-mediated innovation of root-specific eRNAs as a candidate mechanism that may contribute to Triticeae adaptation and provides a foundational resource for exploiting regulatory variation in cereal crop breeding.
2026-06-22 | GSE284462 | GEO
Project description:Cereal genomes have undergone repeated polyploidization and transposable element (TE) proliferation, collectively generating complex regulatory landscapes. The evolutionary trajectories and functional implications of these landscapes, however, remain largely unexplored. By employing chromatin-bound RNA sequencing across seven cereal species, we systematically mapped 45,952 regulatory element transcripts (RETs), including 32,867 distal RETs corresponding to enhancer RNAs (eRNAs). Our analysis reveals that 56% of lineage-specific eRNAs originate from TE expansions, suggesting TEs as significant reservoirs of species-specific regulatory innovation in cereals. Notably, we uncovered a remarkable similarity in defense-related function, root-specific expression, and TE-derived origin of eRNAs across ancient and recent evolutionary layers of Triticeae, suggesting recurrent recruitment of TE-derived root-associated regulatory elements during Triticeae evolution. Furthermore, we found that young eRNA pairs in hexaploid wheat with high sequence similarity, many originating from RLG_famc8.3 and DTC_famc4.3, exhibit pronounced root specificity and coordinated expression, suggesting a targeted amplification and refinement of the successful ancestral regulatory strategy established after Triticeae divergence. To facilitate community access, we developed Cereal-eRNAdb (http://bioinfo.cemps.ac.cn/Cereal-eRNAdb/), a comprehensive database integrating 69,426 eRNAs with functional annotations across 296 samples. Our work indicates that TE-mediated innovation of root-specific eRNAs as a candidate mechanism that may contribute to Triticeae adaptation and provides a foundational resource for exploiting regulatory variation in cereal crop breeding.
2026-06-22 | GSE284461 | 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