Oryza sativa
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ABSTRACT:
PROVIDER: PRJNA137729 | ENA |
REPOSITORIES: ENA
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Project description:Rice is one of the most important global food crops, and is also a model organism for cereal research 31 . Complete genome sequencing of rice, together with advances in transcriptomics and proteomics, has had a dramatic impact on plant growth and 5 breeding programs 32 . Genomic analysis of DNA methylation in rice has revealed methylation patterns associated with gene bodies and promoters, and the occurrence of high levels of DNA methylation in the centromeric domain 33 . A genome-wide investigation of acetylation in rice revealed that H3K9ac and H3K27ac are mainly enriched at transcription start sites associated with active transcription 34 . Furthermore, global proteome analysis has shown that phosphorylation and succinylation are involved in diverse cellular and metabolic processes 35, 36 . However, despite these considerable advances in our knowledge, additional large-scale analysis of the lysine acetylome in rice is expected to identify many more Kac sites and acetylated proteins in this improtant crop plant. In this study, affinity enrichment and high-resolution LC-MS/MS were used for large-scale analysis of the lysine acetylome in rice variety Nipponbare. In total, 1353 lysine acetylation sites were detected in 866 protein groups in rice seedlings. Proteomic analysis showed that Kac occurs in proteins involved in diverse biological processes with varied cellular functions and subcellular localization.
2017-11-13 | PXD004870 | Pride
Project description:Here, we present OryzaPG-DB, a rice proteome database based on shotgun proteogenomics, which incorporates the genomic features of experimental shotgun proteomics data. This version of the database was created from the results of 27 nanoLC-MS/MS runs on a hybrid ion trap-orbitrap mass spectrometer, which offers high accuracy for analyzing tryptic digests from undifferentiated cultured rice cells. Peptides were identified by searching the product ion spectra against the protein, cDNA, transcript and genome databases from Michigan State University, and were mapped to the rice genome. Approximately 3200 genes were covered by these peptides and 40 of them contained novel genomic features. Users can search, download or navigate the database per chromosome, gene, protein, cDNA or transcript and download the updated annotations in standard GFF3 format, with visualization in PNG format. In addition, the database scheme of OryzaPG was designed to be generic and can be reused to host similar proteogenomic information for other species. OryzaPG is the first proteogenomics-based database of the rice proteome, providing peptide-based expression profiles, together with the corresponding genomic origin, including the annotation of novelty for each peptide.
2016-07-20 | PXD004603 | JPOST Repository
Project description:The profiling was conducted with the Rice 3'-Tiling 135k Microarray designed from 31,439 genes deposited at IRGSP, RAP2 database (http://rapdb.lab.nig.ac.jp). We have identified and characterized a T-DNA insert rice mutant (Osfuct) with loss of α1,3-fucosyltransferase function. Matrix-assisted laser desorption/ionization time-of-flight analyses of the N-glycan revealed the lack of α1,3-fucose in the N-glycan structure of rice Osfuct mutant. The mutant displayed the pleiotropic developmental defects such as diminished growth, shorter plant height, less number of tillers, shorter panicle lengths and internode, impaired anther and pollen development. In addition, the anther was curved, pollen grains shapes were shriveled, pollen viability and pollen number per anther was dramatically decreased in Osfuct mutant. The complementation test of Osfuct mutant clearly exhibited that the phenotype is caused by the loss of α1,3-fucosyltransferase function bescause complementation line is rescued. Transcriptome profiling data revealed that several genes essential in plant developmental processes were significantly altered in Osfuct mutant including protein kinases, transcription factors, genes involved in metabolism, genes related to protein synthesis and hypothetical proteins. Moreover, Osfuct mutant exhibited the enhanced salt insensitivity. Taken together, these findings demonstrated that Osfuct plays a critical role in growth, anther, pollen development and salt stress response.
2018-06-06 | GSE110873 | GEO
Project description:- Pollen tube growth is important process for successful double fertilization, which is critical for grain yield in crop plants. Despite much progress in identification of rapid alkalization factors (RALFs) which serve as ligand for signaling transduction during fertilization in Arabidopsis, there is no functional study of RALF in mono-cotyledon plant. - We functionally characterized two pollen specific RALF in rice (Oryza sativa) using multiple CRISPR/Cas9 induced loss-of-function mutants, peptide treatment, expression analyses, tag reporter lines. - OsRALF17 is specifically expressed in pollen and pollen tube as the strongest level among 41 RALF members in rice. Exogenously applied OsRALF17 inhibits pollen tube germination and elongation at high concentration, but enhances tube elongation at low concentration, indicating the regulation of growth balance. Double mutant of OsRALF17 with OsRALF19 exhibit almost male sterile, with defect on pollen germination and tube elongation. - Our study revealed that functionally-redundant OsRALF17 and 19 peptides binds to the OsMTD2, CrRLK1L family member, and transmits ROS signal for pollen tube germination and integrity maintenance in rice. We provide new insights into the role of RALF and expanding our understanding of the biological role of RALF in regulating rice fertilization.
2023-09-21 | PXD037597 | Pride
Project description:The R-loop is a common chromatin feature presented from prokaryotic to eukaryotic genomes and has been revealed to be involved in multiple cellular processes and associated with many human diseases. Here, we take the advantage of our recently developed ssDRIP-seq method to profile genome-wide R-loop levels and provided a first-hand R-loop atlas of Rice (Oryza sativa) at different developmental stages.
2022-12-10 | GSE120922 | GEO
Project description:Genome-wide gene expression profiling of rice stigma
| PRJNA100133 | ENA
Project description:We created a double loss-of-function/knockout mutant targeting three rice genes simultaneously. The two selected genes are as follows: OsABCG16 (LOC_Os06g51460), OsABCG28 (LOC_Os11g22350). These two ABCGs are strongly transcriptional expressed in the rice mature anthers (stages 13) and bi-/tricelluler pollen. The double mutant of these OsABCGs does not produce self-fertilizing seeds due to the short length of the pollen tube inside the pistil (male-sterile). This data is about mature anther transcriptome data about the double mutant of OsABCGs. We sampled mature anther for the analysis.
2025-03-07 | E-MTAB-14885 | biostudies-arrayexpress
Project description:We created a triple loss-of-function/knockout mutant targeting three rice genes simultaneously. The three selected genes are as follows: OsADF1 (LOC_Os02g44470), OsADF6 (LOC_Os04g46910), and OsADF9 (LOC_Os07g30090). These three ADFs are strongly transcriptional expressed in the rice mature anthers (stages 13) and bi-/tricelluler pollen. The triple mutant of these OsADFs does not produce self-fertilizing seeds due to the short length of the pollen tube (male-sterile). This data is about mature anther transcriptome data about the triple mutant of OsADFs (ADFmT). We sampled mature anther for the analysis.
2024-07-02 | E-MTAB-13557 | biostudies-arrayexpress
Project description:Genome-wide Gene Expression Profiling of Salinity Responsiveness in Rice
| PRJNA253003 | ENA
Project description:Transcriptional profiling of MIT knockdown plants. MIT is a mitochondrial Fe transporter essential for rice growth and development. The goal was to determine the effects of MIT on global rice gene expression.
2011-04-07 | GSE28428 | GEO