Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1108516 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:ChIP-seq data of 5 dpa fibers from GhBES1-Overexpression cotton plants GHBES1-OE-FIBER-CHIP-SEQ
2023-03-01 | GSE226370 | GEO
Project description:Fiber cell initiation and development affect cotton fiber yield and quality. Cotton fiber develops from the ovular epidermis of a seed, and approximately 25-30% of protodermal cells in each cotton ovule develop into fiber. However, the molecular basis for fiber cell development remains elusive. Here, we analyzed single-cell RNA-seq (scRNA-seq) data from over 40,000 cells during early stages of fiber cell development in Upland and Pima cotton and in a naked seed mutant. We found concerted expression changes of 900-1,700 genes in fiber-cell clusters involving gene expression, translation, and peptide biosynthesis, which were substantially delayed or absent in the mutant. Expression of ∼500 and ∼300 genes in Upland and Pima cotton, respectively, was distinguishably different and consistent with overrepresentation of the genes in transcriptional and translational regulation, implying their roles in fiber yield and quality traits. Gene co-expression network analysis (GCNA) of scRNA-seq and scATAC-seq data revealed two modules of fiber gene co-expression networks. One module of the fiber co-expressed genes was associated with elevated chromatin accessibility for transcriptional regulation, whereas the other module of the genes was related to translational regulation and ribosome biogenesis. Indeed, expression of cotton putative translation factor genes was elevated in fiber cell clusters in both Upland and Pima cotton. Finally, cotton transgenic plants expressing promoter::GFP confirmed expression patterns of fiber-expressed GhRDL2_D5 during fiber cell initiation. These single-cell genomic resources provide insights into fiber cell development for breeding and biotechnological improvement of fiber yield and quality in Upland and Pima cotton.
2025-12-02 | GSE282999 | GEO
Project description:For environmental safety, the high concentration of heavy metals in the soil should be removed. Cadmium (Cd), one of the heavy metals polluting the soil while its concentration exceeds 3.4 mg/kg in soil. Potential use of cotton for remediating heavy Cd-polluted soils is available while its molecular mechanisms of Cd tolerance remains unclear in cotton. In this study, transcriptome analysis was used to identify the Cd tolerance genes and their potential mechanism in cotton. Finally 4,627 differentially expressed genes (DEGs) in the root, 3,022 DEGs in the stem and 3,854 DEGs in leaves were identified through RNA-Seq analysis, respectively. These genes contained heavy metal transporter genes (ABC, CDF, HMA, etc.), annexin genes, heat shock genes (HSP) amongst others. Gene ontology (GO) analysis showed that the DEGs were mainly involved in the oxidation-reduction process and metal ion binding. The DEGs mainly enriched in two pathways, the influenza A and the pyruvate pathway. GhHMAD5 protein, containing a heavy-metal domain, was identified in the pathway to transport or to detoxify the heavy ion. GhHMAD5-overexpressed plants of Arabidopsis thaliana showed the longer roots compared with the control. Meanwhile, GhHMAD5-silenced cotton plants showed more sensitive to Cd stress compared with the control. The results indicated that GhHMAD5 gene is remarkably involved in Cd tolerance, which gives us a preliminary understanding of Cd tolerance mechanisms in upland cotton. Overall, this study provides valuable information for the use of cotton to remediate the soil polluted with heavy metals.
2019-04-25 | GSE126671 | GEO