Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR27689651_1.fastq.gz | Fastqsanger.gz | |||
| SRR27689651_2.fastq.gz | Fastqsanger.gz | |||
| SRR27689652_1.fastq.gz | Fastqsanger.gz | |||
| SRR27689652_2.fastq.gz | Fastqsanger.gz | |||
| SRR27689653_1.fastq.gz | Fastqsanger.gz |
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Project description:Anther development, particularly around the time of meiosis, is extremely crucial for plant sexual reproduction. Meanwhile, cell-to-cell communication between somatic (especial tapetum) cells and meiocytes are important for both somatic anther development and meiosis. To investigate possible molecular mechanisms involved in protein activities during anther development, we applied high-resolution mass spectrometry-based proteomic and phosphoproteomic analyses for developing rice (Oryza sativa) anthers around the time of meiosis (RAM). In total, we identified 4,984 proteins and 3,203 phosphoproteins with 8,973 unique phosphorylation sites (p-sites). Among those detected here, 1,544 phosphoproteins are currently absent in the Plant Protein Phosphorylation DataBase (P3DB), substantially enriching plant phosphorylation information. Mapman enrichment analysis showed that “DNA repair”, “transcription regulation” and “signalling” related proteins were over-represented in the phosphorylated proteins. Ten genetically identified rice meiotic proteins were detected to be phosphorylated at a total of 25 p-sites; moreover more than 400 meiotically expressed proteins were revealed to be phosphorylated and their phosphorylation sites were precisely assigned. 163 putative secretory proteins, possibly functioning in cell-to-cell communication, are also phosphorylated. Furthermore, we showed that DNA synthesis, RNA splicing and RNA-directed DNA methylation pathways are extensively affected by phosphorylation. In addition, our data support forty-six kinase-substrate pairs predicted by the rice Kinase-Protein Interaction Map, with SnRK1 substrates highly enriched. Taken together, our data revealed extensive protein phosphorylation during anther development, suggesting an important post-translational modification mechanism for protein activity.
2021-01-13 | PXD002756 | Pride
Project description:The genome-wide transcriptome analyses using microarray probes containing genes and repeat sequences have been performed to examine response to the low-temperature in rice. We have particularly focused on the rice anther at the booting stage, since the low-temperature at this stage resulted in pollen abortion. The results demonstrated that the low-temperature stress caused genome-wide changes of transcriptional activities not only in genes, but also in repeat sequences of the rice anther. The degrees of the temperature responsive changes varied among the rice strains.
2013-08-06 | GSE49561 | GEO
Project description:RNA-Seq of rice anther and pollen at anthesis stage
| PRJEB32629 | ENA
Project description:The rice anther transcriptomes responded to low temperature [RNA-seq]
| PRJNA1128161 | ENA
Project description:Background – In flowering plants, the anther is the site of male gametophyte development. Two major events in the development of the male germline are meiosis and the asymmetric division in the male gametophyte that gives rise to the vegetative and generative cells, and the following mitotic division in the generative cell that produces two sperm cells. Anther transcriptomes have been analyzed at progressive stages of development by using microarray and sequence by synthesis technologies to identify genes that regulate anther development. Here we have carried out a comprehensive analysis of rice anther transcriptomes at four distinct stages of development with a focus to identify regulatory components contributing to male meiosis and germline development. Further, these transcriptomes have been compared with transcriptomes of 10 stages of rice vegetative and seed development to identify genes that express specifically during anther development. Results - To understand the molecular processes that lead to male gametophyte development, transcriptome profiling of four stages of anther development in rice [pre-meiotic (PMA), meiotic (MA), anthers at single-celled (SCP) and tri-nucleate pollen (TPA)] was conducted. Around 22,000 genes were found to be expressed in at least one of the anther developmental stages, with the highest number in MA (18,090) and lowest (15,465) in TPA. Comparison of these transcriptome profiles to an in-house generated microarray-based transcriptomics database comprising of 10 stages/tissues of vegetative as well as reproductive development in rice resulted in the identification of 1,000 genes that are specifically expressed in anther stages. Of them the expression of 453 genes was found to be specific to TPA, whereas 78 and 184 genes were expressed specifically in MA and SCP. Gene ontology and pathway analysis of specifically expressed genes revealed that transcription factors and protein folding, sorting and degradation pathway genes dominated in MA, whereas in TPA, those coding for cell structure and signal transduction components were in abundance. Interestingly, about 50% of the genes with anther-specific expression have not been annotated so far. Conclusions - These data not only provide the transcriptome constituents of four landmark stages of anther development but also identify genes that express exclusively in these stages and therefore may contribute to specific aspects of anther and/or male gametophyte development in rice. Moreover, these gene sets assist in building a deeper understanding of underlying regulatory networks and in selecting candidates for gene function validation.
2011-06-10 | GSE27726 | GEO
Project description:Dissection of the genetic pathways and mechanisms by which anther development occurs in grasses is crucial for both a basic understanding of plant development and for traits of agronomic importance like male sterility. In rice, MULTIPLE SPOROCYTES1 (MSP1), a leucine-rich-repeat receptor kinase, play an important role in anther development by limiting the number of sporocytes. OsTDL1a (a TPD1-like gene in rice) encodes a small protein which acts as a cofactor of MSP1 in the same regulatory pathway. In this study, we analyzed small RNA and mRNA changes in different stages of spikelets from wildtype rice, and from msp1 and ostdl1a mutants. Analysis across different stages of rice spikelets of the small RNA data identified miRNAs demonstrating differential abundances. miR2275 was depleted in the two rice mutants; this miRNA is specifically enriched in anthers and functions to trigger the production of 24-nt phased secondary siRNAs (phasiRNAs) from PHAS loci. We observed that the 24-nt phasiRNAs as well as their precursor PHAS mRNAs were also depleted in the two mutants. Based on comparisons of transcript levels across the spikelet stages and mutants, we identified 22 transcription factors as candidates to have roles specific to anther development, potentially acting downstream of the OsTDL1a-MSP1 pathway. An analysis of co-expression identified three Argonaute-encoding genes (OsAGO1d, OsAGO2b, and OsAGO18) that accumulate transcripts coordinately with phasiRNAs, suggesting a functional relationship. By mRNA in situ analysis, we demonstrated a strong correlation between the spatiotemporal pattern of accumulation of these OsAGO transcripts with previously-published phasiRNA accumulation patterns from maize. Raw files for smallRNA-Seq were not provided by submitter.
2016-09-23 | GSE77300 | GEO