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Oryza sativa Japonica Group strain:Nipponbare

ABSTRACT: Analysis of the transgene specification of MucoRice-CTB strain 19A

PROVIDER: PRJDB13597 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	DRR376734_1.fastq.gz	Fastqsanger.gz
	DRR376734_2.fastq.gz	Fastqsanger.gz

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Oryza sativa Japonica Group

Project description:Comparative analysis of genetic alteration between MucoRice-CTB Seed bank and Working seed strains

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Oryza sativa Japonica Group transcriptome sequencing

Project description:Phosphate starvation/sufficient rice seedling, root or shoot Pi-starvation or Pi-sufficient stresses responsible rice genes, including previously unannotated genes were identified by Illumina mRNA-seq technology. 53 million reads from Pi-starvation or Pi-sufficient root or shoot tissues were uniquely mapped to the rice genome, and these included 40574 RAP3 transcripts in root and 39748 RAP3 transcripts in shoot. We compared our mRNA-seq expression data with that from Rice 44K oligomicroarray, and about 95.5% (root) and 95.4% (shoot) transcripts supported by the array were confirmed expression both by the array and by mRNA-seq, Moreover, 11888 (root) and 11098 (shoot) RAP genes which were not supported by array, were evidenced expression with mRNA-seq. Furthermore, we discovered 8590 (root) and 8193 (shoot) previously unannotated transcripts upon Pi-starvation and/or Pi-sufficient.

2012-01-06 | E-MTAB-4302 | biostudies-arrayexpress

Classification of rice (Oryza sativa L. Japonica nipponbare) immunophilins (FKBPs, CYPs) and expression patterns under water stress.

Project description:BackgroundFK506 binding proteins (FKBPs) and cyclophilins (CYPs) are abundant and ubiquitous proteins belonging to the peptidyl-prolyl cis/trans isomerase (PPIase) superfamily, which regulate much of metabolism through a chaperone or an isomerization of proline residues during protein folding. They are collectively referred to as immunophilin (IMM), being present in almost all cellular organs. In particular, a number of IMMs relate to environmental stresses.ResultsFKBP and CYP proteins in rice (Oryza sativa cv. Japonica) were identified and classified, and given the appropriate name for each IMM, considering the ortholog-relation with Arabidopsis and Chlamydomonas or molecular weight of the proteins. 29 FKBP and 27 CYP genes can putatively be identified in rice; among them, a number of genes can be putatively classified as orthologs of Arabidopsis IMMs. However, some genes were novel, did not match with those of Arabidopsis and Chlamydomonas, and several genes were paralogs by genetic duplication. Among 56 IMMs in rice, a significant number are regulated by salt and/or desiccation stress. In addition, their expression levels responding to the water-stress have been analyzed in different tissues, and some subcellular IMMs located by means of tagging with GFP protein.ConclusionLike other green photosynthetic organisms such as Arabidopsis (23 FKBPs and 29 CYPs) and Chlamydomonas (23 FKBs and 26 CYNs), rice has the highest number of IMM genes among organisms reported so far, suggesting that the numbers relate closely to photosynthesis. Classification of the putative FKBPs and CYPs in rice provides the information about their evolutional/functional significance when comparisons are drawn with the relatively well studied genera, Arabidopsis and Chlamydomonas. In addition, many of the genes upregulated by water stress offer the possibility of manipulating the stress responses in rice.

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Gene Expression Profiles Deciphering the Pathways of Coronatine Alleviating Water Stress in Rice (Oryza sativa L.) Cultivar Nipponbare (Japonica).

Project description:Coronatine (COR) is a structural and functional analog of methyl jasmonic acid (MeJA), which can alleviate stress on plant. We studied the effects of COR on the drought stress of rice (Oryza sativa L.). Pre-treatment with COR significantly increased the biomass, relative water and proline content, and DPPH (1,1-diphenyl-2-picrylhydrazyl)-radical scavenging activity, decreased the electrolyte leakage and MDA (Malondialdehyde) content in order to maintain the stability of cell membrane. Meanwhile, we determined how COR alleviates water stress by Nipponbare gene expression profiles and cDNA microarray analyses. Seedlings were treated with 0.1 μmol L-1 COR at the three leafed stage for 12 h, followed with 17.5% polyethylene glycol (PEG). Whole genome transcript analysis was determined by employing the Rice Gene Chip (Affymetrix), a total of 870 probe sets were identified to be up or downregulated due to COR treatment under drought stress. Meanwhile, the real-time quantitative PCR (RT-qPCR) method was used to verify some genes; it indicated that there was a good agreement between the microarray data and RT-qPCR results. Our data showed that the differentially expressed genes were involved in stress response, signal transduction, metabolism and tissue structure development. Some important genes response to stress were induced by COR, which may enhance the expression of functional genes implicated in many kinds of metabolism, and play a role in defense response of rice seedling to drought stress. This study will aid in the analysis of the expressed gene induced by COR.

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