Ontology highlight
ABSTRACT:
PROVIDER: PRJNA985128 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR24957700_1.fastq.gz | Fastqsanger.gz | |||
| SRR24957700_2.fastq.gz | Fastqsanger.gz | |||
| SRR24957800_1.fastq.gz | Fastqsanger.gz | |||
| SRR24957800_2.fastq.gz | Fastqsanger.gz | |||
| SRR24967300_1.fastq.gz | Fastqsanger.gz |
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Project description:Common wheat (T. aestivum) converged three subgenomes adapted to different environments. The combinatorial interaction between transcription factors (TFs) and regulatory elements (REs) defines a regulatory circuit that underlies subgenome convergence and divergence. Compared to the relatively conserved gene composition across subgenomes, the intergenic regions with abundant REs is drastically diversified by almost complete TE turnovers, raising major questions regarding how subgenome convergent and divergent regulation is encoded in the highly diversified intergenic regions, and the impact of TE evolution on regulatory conservation and innovation. In the present study, we created genome-wide TF binding catalog to assemble an extensive wheat regulatory network comprising connections among 182 TFs. The different effects of ancient and recent TE insertions on regulatory specificity were observed. Subgenome asymmetric TE expansion is an important source of subgenome divergent TFBS, which help explain the vast occupancy difference across subgenomes. Interestingly, the ancient expansion of RLC_famc1.4-derived TFBS occurred in more than 25% triads promoters. A significant fraction of these TE-derived TFBS subjected to region-specific evolutionary selections, resulting in subgenome-balanced TF binding but unbalanced degeneration of flanking TE sequences. These TE-derived subgenome convergent and divergent regulation linked to subgenome conserved and diversified pathways, suggesting that TEs are an important regulatory driving force contributed to polyploid evolution. Overall, this study demonstrated the impact of TEs on shaping the plasticity and adaptation of common wheat, enriched the theories of TE-promoted transcriptional innovation from the evolutionary aspects of polyploid regulation since first reported by McClintock.
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Project description:Plant-based adhesives, such as the ones made from wheat, have been prominently used for books and paper-based objects and are also used as conservation adhesives. Starch paste originates from starch granules, whereas flour paste encompasses the entire wheat endosperm proteome, offering strong adhesive properties due to gluten proteins. From the conservation perspective, understanding the precise nature of the adhesive is vital, as the longevity, resilience, and reaction to environmental changes can differ substantially between starch and flour-based pastes. We devised a proteomics method to discern the protein content of these pastes. Protocols involved extracting soluble proteins using 0.5 M NaCl and 30 mM Tris-HCl solutions, then targeting insoluble proteins, such as gliadins and glutenins, with a buffer containing 7M urea, 2M thiourea, 4% CHAPS, 40 mM Tris, and 75 mM DTT. Flour paste's proteome is diverse (1942 proteins across 759 groups), contrasting with starch paste's predominant starch-associated protein makeup (218 proteins in 58 groups). Transformation into pastes reduces proteomes' complexity. Testing on historical bookbindings confirmed the use of flour-based glue, rich in gluten and serpins. High levels of deamidation were detected, particularly for glutamine residues, which can impact the solubility and stability of the glue over time.
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