Oryza sativa, Nipponbare RNA-Seq - Conserved Poaceae Specific Genes Project
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ABSTRACT:
ORGANISM(S): Oryza sativa Japonica Group
PROVIDER: E-MTAB-2039 | BioStudies |
REPOSITORIES: biostudies
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Project description:Illumina RNA Sequencing (RNA-Seq) of Oryza sativa, Nipponbare for the Conserved Poaceae Specific Genes project. Authors: Robin Buell, Ning Jiang, Haining Lin, Rebecca Davidson, Malali Gowda, John Hamilton, Brieanne Vaillancourt
2012-04-04 | E-MTAB-2039 | ArrayExpress
Project description:Illumina RNA Sequencing (RNA-Seq) of Oryza sativa, Nipponbare for the Conserved Poaceae Specific Genes project. Authors: Robin Buell, Ning Jiang, Haining Lin, Rebecca Davidson, Malali Gowda, John Hamilton, Brieanne Vaillancourt
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Project description:Gene expression profoling of developping endosperm at 3 and 6 days after flowering (DAH): Nipponbare vs NIL(TGW6) We used two rice varieties, NIL(TGW6) and Nipponbare.NIL(TGW6) is a nearly isogenic line containing the thousand grain weight qTGW6. For samples used three stages: 3 and 6 DAH endosperm in both Nipponbare and NIL(TGW6). Two dye swapped experiments were performed.
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Project description:In the japonica rice strain Gimbozu EG4, the DNA transposon mPing is actively transposing to attain over 1,000 copies, whereas in Nipponbare, where this element is virtually silent and has only 50 copies. To analyze the impact of such a massive amplification of transposable element on gene regulation, we performed the rice 44k oligo microarray analysis. Total RNA was extracted from 7-day-old seedlings of EG4 and Nipponbare plants, grown in a greenhouse at at 26ËC and subjected to 44k oligo-DNA microarray with 4 biological replicates.
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Project description:Nipponbare performs poorly in phosphorus (P) deficient soil whereas a Nipponbare-derived NIL containing the Pup1 allele of donor parent Kasalath is tolerant to P deficiency. In this experiment we compared gene expression patterns in roots of this NIL to Nipponbare, grown either in a P deficient or P fertilized soil. The aim is to separate constitutive differences in expression from those induced by P deficiency. Experiment Overall Design: Total RNA was extrancted from root that were grown under two conditions and prepared three biological replicant in each line (total 6 samples in each line). Experiment Overall Design: We used 6 slides for this experiment, in each slide, Nipponbare and 6-4 samples grown under same condition were hybridized.
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Project description:WRKY45-overexpressing (WRKY45-ox) rice plants are extremely resistant to rice blast and bacterial leaf-blight diseases. To search for the genes that are potentially responsible for the strong resistance, we performed genome-wide gene expression analysis in WRKY45-ox rice. A microarray analysis using Agilent rice oligo microarray for approximately 42,000 rice genes identified 1,664 genes that are upregulated in WRKY45-ox rice compared with non-transformant rice cv. Nipponbare (NB). Analysis of the genes with altered expression in WRKY45-ox rice by a Gene ontology program (Agri GO; http://bioinfo.cau.edu.cn/agriGO/) revealed that several genes in the biosynthetic pathway for diterpenoid phytoalexins, for which anti-blast fungus activities have been reported, were upregulated in WRKY45-ox rice. Nipponbare rice (Oryza sativa) and WRKY45-ox rice were analyzed in three biological replicates.
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Project description:BACKGROUND:Rice research has been enabled by access to the high quality reference genome sequence generated in 2005 by the International Rice Genome Sequencing Project (IRGSP). To further facilitate genomic-enabled research, we have updated and validated the genome assembly and sequence for the Nipponbare cultivar of Oryza sativa (japonica group). RESULTS:The Nipponbare genome assembly was updated by revising and validating the minimal tiling path of clones with the optical map for rice. Sequencing errors in the revised genome assembly were identified by re-sequencing the genome of two different Nipponbare individuals using the Illumina Genome Analyzer II/IIx platform. A total of 4,886 sequencing errors were identified in 321 Mb of the assembled genome indicating an error rate in the original IRGSP assembly of only 0.15 per 10,000 nucleotides. A small number (five) of insertions/deletions were identified using longer reads generated using the Roche 454 pyrosequencing platform. As the re-sequencing data were generated from two different individuals, we were able to identify a number of allelic differences between the original individual used in the IRGSP effort and the two individuals used in the re-sequencing effort. The revised assembly, termed Os-Nipponbare-Reference-IRGSP-1.0, is now being used in updated releases of the Rice Annotation Project and the Michigan State University Rice Genome Annotation Project, thereby providing a unified set of pseudomolecules for the rice community. CONCLUSIONS:A revised, error-corrected, and validated assembly of the Nipponbare cultivar of rice was generated using optical map data, re-sequencing data, and manual curation that will facilitate on-going and future research in rice. Detection of polymorphisms between three different Nipponbare individuals highlights that allelic differences between individuals should be considered in diversity studies.
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Project description:BACKGROUND:Genomic sequence of a rice cultivar Nipponbare has been often used as a reference sequence since a whole-genomic sequence was first determined in 2005 by the International Rice Genome Sequencing Project. As for mitochondrial genomic sequence of Nipponbare, two groups have deposited their sequences into DDBJ/EMBL/GenBank under the accession numbers BA000029 and DQ167400. However, there are 19 discrepancies in the nucleotide sequences of 7 genes between BA000029 and DQ167400. FINDINGS:We performed PCR to amplify these 7 genes and to perform direct sequencing. Nucleotides of the discrepant sites were all identical to those in DQ167400.1. The sequence in BA000029.3 is thought to contain sequencing errors. CONCLUSION:Nucleotide sequences of the mitochondrial genes in BA000029.3 need to be updated using the data in this study when used as a reference genome.
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Project description:To better understand the complex mechanisms regulating Pi homeostasis in rice (Oryza sativa L. cv. Nipponbare), a time course experiment was performed, where pre-germinated seedlings were grown hydroponically for two weeks on Pi-sufficient medium (0.32 mM Pi), before transferring half of the plants to Pi-deficient solution (0 mM Pi) for 21 days (d). After three weeks of Pi-starvation treatment, half of these plants where then re-supplied with Pi sufficient media for up to 24 hours (h). In total, nine time points were selected in order to cover short and long term responses to Pi starvation as well as the effects of Pi re-supply on Pi starved plants.
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