Project description:Whole Genome Metabolism of "Oryza sativa Japonica Group"
This is a whole genome metabolism model of Oryza sativa Japonica Group.
This model has been automatically generated by the SuBliMinaL Toolbox
and libAnnotationSBML using information coming from from KEGG (release 66, April 2013, accessed via the resource's web services interface) and, where relevant, augmented with metabolic pathway information extracted from MetaCyc (version 17.0, March 2013).
This model has been produced by the path2models
project and is currently hosted on BioModels Database
and identified by: BMID000000141346
Other models with the same genus include BMID000000022012 BMID000000022013 BMID000000022014 BMID000000022015 BMID000000022016 BMID000000022017 BMID000000022018 BMID000000022019 BMID000000022020 BMID000000022021 BMID000000022022 BMID000000022023 BMID000000022024 BMID000000022025 BMID000000022026 BMID000000022027 BMID000000022028 BMID000000022029 BMID000000022030 BMID000000022031 BMID000000022032 BMID000000022033 BMID000000022034 BMID000000022035 BMID000000022036 BMID000000022037 BMID000000022038 BMID000000022039 BMID000000022040 BMID000000022041 BMID000000118664 BMID000000118665 BMID000000118666 BMID000000118667 BMID000000118668 BMID000000118669 BMID000000118670 BMID000000118671 BMID000000118672 BMID000000118673 BMID000000118674 BMID000000118675 BMID000000118676 BMID000000118677 BMID000000118678 BMID000000118679 BMID000000118680 BMID000000118681 BMID000000118682 BMID000000118683 BMID000000118684 BMID000000118685 BMID000000118686 BMID000000118687 BMID000000118688 BMID000000118689 BMID000000118690 BMID000000118691 BMID000000118692 BMID000000118693 BMID000000118694 BMID000000118695 BMID000000118696 BMID000000118697 BMID000000118698 BMID000000118699 BMID000000118700 BMID000000118701 BMID000000118702 BMID000000118703 BMID000000118704 BMID000000118705 BMID000000118706 BMID000000118707 BMID000000118708 BMID000000118709 BMID000000118710 BMID000000118711 BMID000000118712 BMID000000118713 BMID000000118714 BMID000000118715 BMID000000118716 BMID000000118717 BMID000000118718 BMID000000118719 BMID000000118720 BMID000000118721 BMID000000118722 BMID000000118723 BMID000000118724 BMID000000118725 BMID000000118726 BMID000000118727 BMID000000118728 BMID000000118729 BMID000000118730 BMID000000118731 BMID000000118732 BMID000000118733 BMID000000118734 BMID000000118735 BMID000000118736 BMID000000118737 BMID000000118738 BMID000000118739 BMID000000118740 BMID000000118741 BMID000000118742 BMID000000118743 BMID000000118744 BMID000000118745 BMID000000118746 BMID000000118747 BMID000000118748 BMID000000118749 BMID000000118750 BMID000000118751 BMID000000142467 .
To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication
for more information.
Project description:The present study quantifies the transcriptomes of wild-type and transgenic Ubi::OsYHB rice seedlings (in the genetic background of Oryza sativa ssp. japonica CV Nipponbare) grown in the dark or under continous red light (Rc, at 50 µmol m-2 s-1) conditions. Overall design: WT (Nipponbare cultivar; Nip) and Ubi::OsYHB/Nip transgenic seedlings were grown at 28°C for 5 days in darkness or under continuous red light at 50 µmol m-2 s-1 (Rc50). Seedlings were harvested in subjective morning, immediately frozen in liquid nitrogen and strored at -80°C until RNA extraction. The expression of OsYHB is driven by the maize Ubiquitin promoter. Two biological replicates for each treatment. Two independent, genetically single-insertion, homozygous Ubi::OsYHB/Nip lines (#1 and # 9, with determined 41- and 23-fold overexpression levels of OsYHB in comparison to the wild-type control, respectively) were used. GeneChip 3' IVT Express Kit (Affymetrix) was used to synthesize and label aRNA.
Project description:The allene oxide synthase (AOS) branch and the hydroperoxide lyase (HPL) branch of the oxylipin pathway function in plant responses to diverse stresses and have potential cross-talks between each other in the biosynthesis and signaling regulation, but there is still an absence of direct evidence and detailed information about this communication. Here, we identified and characterized a jasmonates acid (JA) overproduction mutant, cea62, by screening the Constitutive Expression of AOS gene (cea) from rice T-DNA insertion mutant library. Map-based cloning was used to isolate the target gene as the hydroperoxide lyase OsHPL3 gene. The gene expression, HPL enzyme activity and its resulting products, (E)-2-hexenal, were all depleted in the cea62 mutant, which resulted in dramatic JA overproduction and activation of JA signaling in the mutant. Consistent with the formation of the lesion mimic phenotype and the timing of the induction for some defense responsive genes, the activation of JA biosynthesis and signaling was regulated in a developmental way, just as the way by which OsHPL3 was regulated in the wild type plant. Microarray data showed that the JA-governed defense response was greatly activated in the cea62 mutant plant and the cea62 plant obtained enhanced resistance to the bacterial blight pathogen Xanthomonasoryzaepvoryzae (Xoo) T1 strain. Wounding response was attenuated in the cea62 mutant at an early developmental stage, while it was partially recovered when JA levels were elevated at a later developmental stage in the cea62 mutant. But, the wounding response was not altered at different developmental stages in the wild type plant. These findings suggest that these two branches of the oxylipin pathways crosstalked in the biosynthesis and signaling pathways and cooperated with each other to function in diverse stress responses. We compared the gene expression profile in leaf tissues of the wild-type plant and the cea62 mutant after lesion mimic phenotype appeared two months after sowing. Total RNAs were extracted from leaf blades from the rice (Oryza sativa L.) wild-type Nipponbare plant and from leaf blades of the rice (Oryza sativa L.) cea62 mutant in the Nipponbare (ssp japonica) background at two months after sowing. Three replicates of the cea62 mutant and wild type were performed.
Project description:Oryza sativa Indica group IR29 (salt sensitive) seedlings were subjected to salt stress or control conditions and sampled at five time points over the course of 24 hours. RNA samples extracted were assayed using the Illumina HiSeq 2000 platform.
Project description:Expression in seven tissues from Oryza sativa L. ssp japonica Nipponbare was profiled using RNA-sequencing: callus, leaf, root, seed, shoot, panicle before flowering, and panicle after flowering. The original experiment examined gene expression in the seven tissues, and utilized the data both to compare gene expression patterns between retrogenes and their parents and to compare patterns of expression divergence between RNA-based duplicates and DNA-based duplicates Note: All samples in SRA were assigned the same sample accession (DRS000668). This is incorrect as there are different samples, hence “Source Name” was replaced with new values. Comment[ENA_SAMPLE] contains the original SRA sample accessions.
Project description:Oryza sativa L. Japonica nipponbare seedlings were treated with 300mM NaCl or water, and then samples were taken after one hour, five hours and 24 hours, to assess which genes are differentially expressed over time during salt stress treatment. The results from this dataset are also compared with those from the same samples assayed using RNA-seq.