Ontology highlight
ABSTRACT:
PROVIDER: PRJNA839214 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Soybean is a critical source of vegetable protein, yet its proteome remains under-characterized. Here, we quantify 12,855 proteins across 14 soybean organs using 4D-data-independent acquisition mass spectrometry (4D-DIA-MS), creating the most extensive soybean proteome dataset to date. Organ-specific protein expression and co-expression analyses highlight functional specificity, with significant differences in protein-transcript abundance across organs. We also map N6-methyladenosine (m6A) modifications, identifying their key role in post-transcriptional protein regulation. Integrative analysis of proteome and m6A methylome identifies novel regulator in m6A methylation. This comprehensive proteomic and m6A landscape advances our understanding of soybean biology and provides a valuable resource for crop improvement.
2025-05-18 | GSE262990 | GEO
Project description:<p>Pigmented rice (<em>Oryza sativa L.</em>) is a rich source of nutrients, but pigmented lines typically have long life cycles and limited productivity. Here we generated genome assemblies of 5 pigmented rice varieties and evaluated the genetic variation among 51 pigmented rice varieties by resequencing an additional 46 varieties. Phylogenetic analyses divided the pigmented varieties into four varietal groups: Geng-japonica, Xian-indica, circum-Aus and circum-Basmati. Metabolomics and ionomics profiling revealed that black rice varieties are rich in aromatic secondary metabolites. We established a regeneration and transformation system and used CRISPR-Cas9 to knock out three flowering time repressors (Hd2, Hd4 and Hd5) in the black Indonesian rice Cempo Ireng, resulting in an early maturing variety with shorter stature. Our study thus provides a multi-omics resource for understanding and improving Asian pigmented rice.</p>
2023-03-27 | MTBLS3320 | MetaboLights
Project description:Intercropping is a sustainable agricultural practice widely used around the world for enhancing resource use efficiency. However, short crops often grow in shade condition underneath the canopy of tall crops. Soybean is one of the most important oil crops and usually is planted in intercropping patterns. However, little is known about the acclimation responses of soybean leaves to shade in intercropping condition at the transcriptome level.
2013-07-11 | E-MTAB-4279 | biostudies-arrayexpress
Project description:Soybean is a critical source of vegetable protein, yet its proteome remains under-characterized. Here, we quantify 12,855 proteins across 14 soybean organs using 4D-data-independent acquisition mass spectrometry (4D-DIA-MS), creating the most extensive soybean proteome dataset to date. Organ-specific protein expression and co-expression analyses highlight functional specificity, with significant differences in protein-transcript abundance across organs. We also map N6-methyladenosine (m6A) modifications, identifying their key role in post-transcriptional protein regulation. Integrative analysis of proteome and m6A methylome identifies novel regulator in m6A methylation. This comprehensive proteomic and m6A landscape advances our understanding of soybean biology and provides a valuable resource for crop improvement.
2024-01-18 | PXD048672 |
Project description:MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs (19–24 nt) that regulates de gene expression, mainly through mRNA targets cleavage and translation inhibition. In plants, miRNAs have been shown to play pivotal roles in a wide variety of metabolic and biological processes like plant growth, development, and response to biotic and abiotic stress. Soybean is one of the most important crops worldwide, due to the production of oil and its high protein content. The reproductive phase is considered the most important for the yield of soybean, which is mainly intended to produce the grains. The identification of miRNAs is not yet saturated in soybeans, and there are no studies linking them to the different floral organs. In this study, three different soybean floral whorls were used in the construction of sRNA libraries. The sequencing of petal, carpel and stamen libraries by the Solexa platform generated a total of 10,165,661 sequences. Subsequently analyses detected 200 miRNAs sequences, from those 41 were novel miRNAs never detected before, 80 were conserved soybean miRNAs, 31 were new antisense conserved soybean miRNAs and 46 soybean miRNAs isoforms. We also found a new miRNA conserved in other plant species, and finally one miRNA-sibling of a soybean conserved miRNA. Conserved and novel miRNAs were evaluated by RT-qPCR. We observed a differential expression across the three whorls for six miRNAs analyzed. A computational prediction of targets for miRNAs analyzed by RT-qPCR was performed. Many of the predicted targets have described functions related to the reproductive process in plants. In summary, the increased accumulation of specific and novel miRNAs in different whorls indicates that miRNAs are an important part of the regulatory network in soybean flower.
2018-05-25 | GSE69572 | GEO