Oryza sativa, Oryza rufipogon
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ABSTRACT:
PROVIDER: PRJNA407820 | ENA |
REPOSITORIES: ENA
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Project description:Dongxiang wild rice (Oryza rufipogon Griff.) is the progenitor of cultivated rice (Oryza sativa L.) and is well known for its superior level of tolerance against cold, drought and diseases. To date, however, little is known about the salt-tolerant character of Dongxiang wild rice. To elucidate the molecular genetic mechanisms of salt-stress tolerance in Dongxiang wild rice, the Illumina HiSeq 2000 platform was used to analyze the transcriptome profiles of the leaves and roots at the seedling stage under salt stress compared with those under normal conditions. The analysis results for the sequencing data showed that 6,867 transcripts were differentially expressed in the leaves (2,216 up-regulated and 4,651 down-regulated) and 4,988 transcripts in the roots (3,105 up-regulated and 1,883 down-regulated). Among these differentially expressed genes, the detection of many transcription factor genes demonstrated that multiple regulatory pathways were involved in salt stress tolerance. In addition, the differentially expressed genes were compared with the previous RNA-Seq analysis of salt-stress responses in cultivated rice Nipponbare, indicating the possible specific molecular mechanisms of salt-stress responses for Dongxiang wild rice. A large number of the salt-inducible genes identified in this study were co-localized onto fine-mapped salt-tolerance-related quantitative trait loci, providing candidates for gene cloning and elucidation of molecular mechanisms responsible for salt-stress tolerance in rice.
2016-01-13 | GSE73181 | GEO
Project description:GBS data of various accessions of Oryza rufipogon (species of wild rice) and an elite cultivar of O. sativa (Asian cultivated rice) Genome sequencing
| PRJNA808887 | ENA
Project description:Dongxiang wild rice (Oryza rufipogon Griff.) is the progenitor of cultivated rice (Oryza sativa L.) and is well known for its superior level of tolerance against cold, drought and diseases. To date, however, little is known about the salt-tolerant character of Dongxiang wild rice. To elucidate the molecular genetic mechanisms of salt-stress tolerance in Dongxiang wild rice, the Illumina HiSeq 2000 platform was used to analyze the transcriptome profiles of the leaves and roots at the seedling stage under salt stress compared with those under normal conditions. The analysis results for the sequencing data showed that 6,867 transcripts were differentially expressed in the leaves (2,216 up-regulated and 4,651 down-regulated) and 4,988 transcripts in the roots (3,105 up-regulated and 1,883 down-regulated). Among these differentially expressed genes, the detection of many transcription factor genes demonstrated that multiple regulatory pathways were involved in salt stress tolerance. In addition, the differentially expressed genes were compared with the previous RNA-Seq analysis of salt-stress responses in cultivated rice Nipponbare, indicating the possible specific molecular mechanisms of salt-stress responses for Dongxiang wild rice. A large number of the salt-inducible genes identified in this study were co-localized onto fine-mapped salt-tolerance-related quantitative trait loci, providing candidates for gene cloning and elucidation of molecular mechanisms responsible for salt-stress tolerance in rice. Leaf and root mRNA profiles of Dongxiang wild rice at the seedling stage with or without salt stress were generated by deep sequencing, on Illumina Hiseq 2000 platform.
2016-01-13 | E-GEOD-73181 | biostudies-arrayexpress
Project description:Iron (Fe) is an essential micronutrient for almost all organisms. However, Fe is frequently inaccessible to plants. To acquire insoluble Fe from soil, rice (Oryza sativa L.) plants employ a Combined Strategy, which is composed by all features of Strategy II, common to all Poaceae species, and some features of the Strategy I from non-Poaceae. To understand the evolution of Fe uptake mechanisms, we analyzed the root transcriptomic response to Fe deficiency in two species from the Oryza genus: O. sativa and its wild progenitor O. rufipogon. A total of 622 and 2,017 genes were found to be differentially expressed in O. sativa and O. rufipogon, respectively. Among the genes regulated in both species, we found the Fe transporters associated with Strategy I, such as IRT1, IRT2 and NRAMP1; and genes associated with Strategy II, such as YSL15 and IRO2.
2019-11-19 | GSE131238 | GEO
Project description:We describe a more detailed survey undertaken to detect candidate CNVs in a panel of 20 Asian cultivated rice and the genome-wide characteristics of CNVs in subspecies and groups. These resources allowed us to analyze genetic structure as indicated by CNVs, to implicate the biological roles of CNVs, and to identify candidate CNVs that are likely to occur independently in groups and contribute to differences between the subspecies.
2014-01-01 | GSE42769 | GEO
Project description:Genomic dissection of small RNAs in wild rice (O.rufipogon): lessons for rice domestication [degradome]
| PRJNA170713 | ENA
Project description:Genomic dissection of small RNAs in wild rice (O.rufipogon): lessons for rice domestication [small RNA]
| PRJNA170714 | ENA
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:Cultivated rice (Oryza sativa L.) is frequently exposed to multiple stresses, including Schizotetranychus oryzae mite infestation. Rice domestication has narrowed the genetic diversity of the species, leading to a wide susceptibility. This work aimed to observe the response of two wild rice species (Oryza barthii and O. glaberrima) and two O. sativa genotypes (cv. Nipponbare and f. spontanea) to S. oryzae infestation. Surprisingly, leaf damage, histochemistry, chlorophyll concentration and fluorescence showed that the wild species present higher level of leaf damage, increased accumulation of H2O2 and lower photosynthetic capacity when compared to O. sativa genotypes under infested conditions. Infestation decreased tiller number, except in Nipponbare. Infestation also caused the death of wild plants during the reproductive stage. While infestation did not affect the weight of 1,000 grains in both O. sativa genotypes, the number of panicles per plant was affected only in f. spontanea, and the percentage of full seeds per panicle and seed length were increased only in Nipponbare. Using proteomic analysis, we identified 195 differentially abundant proteins when comparing susceptible (O. barthii) and tolerant (Nipponbare) genotypes under control and infested conditions. O. barthii has a less abundant antioxidant arsenal and is unable to modulate proteins involved with general metabolism and energy production under infested condition. Nipponbare presents high abundance of detoxification-related proteins, general metabolic processes and energy production, suggesting that, under infested condition, the primary metabolism is maintained more active compared to O. barthii. Also, under infested conditions, Nipponbare presents higher levels of proline and a greater abundance of defense-related proteins, such as osmotin, ricin B-like lectin, and protease inhibitors. These differentially abundant proteins can be used as biotechnological tools in breeding programs aiming increased tolerance to mite infestation.
2021-09-09 | PXD020940 | Pride