Small RNAs in stress-related rice cultivars
Ontology highlight
ABSTRACT:
ORGANISM(S): Oryza sativa
PROVIDER: GSE64651 | GEO | 2015/12/31
SECONDARY ACCESSION(S): PRJNA271566
REPOSITORIES: GEO
Similar Datasets
Project description:In this study, we sequenced small RNA content from three different rice cultivars employing Illumina technology. More than 15 million reads were generated using Illumina high-throughput sequencing platform. After pre-processing, distinct small RNA sequences were identified for each rice cultivars. We collected seedlings of different rice cultivars and total RNA isolated was subjected to Illumina sequencing. The sequenced data was further filtered using NGS QC Toolkit to obtain high-quality reads. The filtered reads were pre-processed using modified perl script provided in the miRTools software. After quality control, the identical reads were collapsed into a unique read and read count for each sequence was recorded. All the filtered unique reads from each sample were mapped on the rice genome to find their location.
2015-12-31 | E-GEOD-64651 | biostudies-arrayexpress
Project description:In this study, we aim to present a global view of transcriptome dynamics in different rice cultivars (IR64, Nagina 22 and Pokkali) under control and stress conditions. More than 50 million high quality reads were obtained for each tissue sample using Illumina platform. Reference-based assembly was performed for each rice cultivar. The transcriptome dynamics was studied by differential gene expression analyses between stress treatment and control sample.
2015-12-31 | GSE60287 | GEO
Project description:In this study, we aim to present a global view of transcriptome dynamics in different rice cultivars (IR64, Nagina 22 and Pokkali) under control and stress conditions. More than 50 million high quality reads were obtained for each tissue sample using Illumina platform. Reference-based assembly was performed for each rice cultivar. The transcriptome dynamics was studied by differential gene expression analyses between stress treatment and control sample. We collected seedlings of three rice cultivars subjected to control (kept in water), desiccation (transferred on folds of tissue paper) and salinity (transferred to beaker containing 200 mM NaCl solution) treatments. Total RNA isolated from these tissue samples was subjected to Illumina sequencing. The sequence data was further filtered using NGS QC Toolkit to obtain high-quality reads. The filtered reads were mapped to Japonica reference genome using Tophat software. Cufflinks was used for reference-based assembly and differential gene expression was studied using cuffdiff software. The differentially expressed genes during various abiotic stress conditions were identified.
2015-12-31 | E-GEOD-60287 | biostudies-arrayexpress
Project description:In this study, we aim to generate genome-scale DNA methylation profiles at single-base resolution in different rice cultivars (IR64, Nagina 22 and Pokkali) under control and stress conditions. Using high-throughput whole genome bisulfite Sequencing, we generated DNA methylation maps covering the vast majority of cytosines in the rice genome. More than 152 million high quality reads were obtained for each tissue sample using Illumina platform. We discovered extensive DNA methylation in rice cultivars, identified the context and level of methylation at each site.Numerous differentially methylated regions (DMRs) among different cultivars under control and stress conditions were identified and many of them were associated with differential gene expression. The high resolution methylome maps of different rice genotypes and differentially methylated regions will serve as reference for understanding the epigenetic regulation of stress responses in plants.
2015-12-31 | GSE60288 | GEO
Project description:In this study, we aim to generate genome-scale DNA methylation profiles at single-base resolution in different rice cultivars (IR64, Nagina 22 and Pokkali) under control and stress conditions. Using high-throughput whole genome bisulfite Sequencing, we generated DNA methylation maps covering the vast majority of cytosines in the rice genome. More than 152 million high quality reads were obtained for each tissue sample using Illumina platform. We discovered extensive DNA methylation in rice cultivars, identified the context and level of methylation at each site.Numerous differentially methylated regions (DMRs) among different cultivars under control and stress conditions were identified and many of them were associated with differential gene expression. The high resolution methylome maps of different rice genotypes and differentially methylated regions will serve as reference for understanding the epigenetic regulation of stress responses in plants. Whole genome bisulfite sequencing of seven control/stressed samples from three rice cultivars (IR64, N22 and Pokkali)
2015-12-31 | E-GEOD-60288 | biostudies-arrayexpress
Project description:Purpose: To study the differential gene expression by comparing resistant and susceptible rice cultivars against the rice blast fungus M. Oryzae. Methods: Rice leaves were collected after M. Oryzae (MO36) infection from resistant and susceptible cultivars, preserved on deep freezer on -80O C frozen on liquid nitrogen, Total RNA from rice plant tissues was extracted using RNeasy Plant Mini Kit (Qiagen) by following manufacturer protocol. RNA libraries were prepared for sequencing using standard Illumina protocols. Results: Around 35 million pairs of filtered 150 base paired reads were obtained for each biological sample. These reads were mapped against RGAP7 using reference assembly tool of CLC Genomics Workbench. The mapped read data was summarised in to a matrix for each sample. count data was compared between the samples to identify the differentially expressed genes. genes were further filtered based on fold change, p value and FDR p value. The count data was further statistically analysed using Kal's Z test integrated into CGWB. Genes exhibiting 3 fold change and FDR p value <0.05 were filtered as either up regulated or down regulated gene. we obtained 7577 and 4290 significant (FDR adjusted p value ≤0.05) differentially expressed locus id in the resistant and susceptible rice cultivars, respectively . The number of significant DEL with fold change value greater and less than 3 were 3523 upregulated 4054 downregulated and 2190 upregulated & 2100 downregulated in resistance and susceptible cultivars, respectively. 2-way and and 4-way upregulated and downregulated gene comparisions was carried out. To identify the changes in biological process and molecular function the pathway and gene set enrichment analysis was performed in resistant BR2655 and susceptible HR12 rice cultivars. Conclusions: This study represents the first transcriptome analysis of resistant BR2655 and susceptible HR12 upon M.oryzae infection, generated by RNA-seq technology. This transcriptome analysis further helps to understand the differential gene expression analysis response to the M.oryzae. And candidate genes which are involved in triggering defense mechanism in rice plants. Further it helps to understand the mechanism of activating a cascade of defense responses in resistant and susceptible plants.
2024-06-01 | GSE192588 | GEO
Project description:To understand the evolution of imprinting mechanisms in the rice species Oryza sativa, we analyzed DNA methylation, transcription and small RNA expression in embryo and endosperm. Cultivars chosen to represent the genetic diversity of cultivated Oryza sativa comprised Nipponbare and Kitaake of the japonica subspecies, and IR64 and 93-11 cultivars of the indica subspecies. While imprinted expression is generally conserved among rice cultivars, approximately 10% of imprinted genes show imprinting divergence across the four cultivars. Analyses of DNA methylation and small RNAs revealed that small RNA producing loci are closely associated with genic regions and four times more likely to be imprinted than genes. However, imprinting divergence most often correlated with DNA methylation epimutations. Correlative epialleles were largely stable within subspecies. Small indels and transposable element insertions were found at half of the epimutated loci and associated with imprinting divergence at half of the remaining loci. Correlating epigenetic and genetic variation occurred at key regulatory regions – the promoter and transcription start site of maternally-biased genes, and the promoter and gene body of paternally-biased genes. Our results reinforce models for the role of maternal-specific DNA hypomethylation in imprint formation at both maternally and paternally biased genes, and highlight the role of transposition events and epimutation in rice imprinting evolution.
2021-06-29 | GSE130122 | GEO
Project description:We aimed to identify putative ABA-regulated miRNAs expressed in rice by using a deep sequencing approach developed by Solexa (Illumina). Two small RNA libraries were constructed from Osaba1-1 and wild type rice leaves, and more than ten million small RNA sequence reads were generated for each library. We identified 13 ABA-regulated miRNAs via expression profiling of the miRNAs based on a comparative miRNAomic analysis in combination with experimental validation. To the best of our knowledge, this is the first report of a systematic investigation of ABA-regulated miRNAs and their targets in rice.
2015-05-31 | GSE63367 | GEO
Project description:The lack of MIRNA set and genome sequence of O. rufipogon (the ancestor of the cultivated rice) has limited to answer the role of MIRNA genes in rice domestication. In this study, a genome, three small RNA populations and a degradome of O.rufipogon were sequenced by Illumina platform and miRNA expression were investigated by miRNA chips. A de novo genome was assembled using ~55x coverage of raw sequencing data and a total of 387 MIRNAs were identified in the O. rufipogon genome based on ~5.2 million unique small RNA reads from three different tissues of O. rufipogon. Of these O. rufipogon MIRNAs, 259 were not found in the cultivated rice, suggesting loss of these MIRNAs in the cultivated rice. We also found that 48 MIRNAs were novel in the cultivated rice, suggesting that they were potential targets of domestication selection. Some miRNAs showed significant expression difference in the wild and cultivated rice, suggesting that expression of miRNA could also be a target of domestication, as demonstrated for the miR164 family. Our results illustrated MIRNA genes, like protein-coding genes, were significantly shaped during rice domestication and could be one of the driven forces contributed to rice domestication. Non-coding small RNA were generated from three different tissues of O.rufipogon by sequecing using Illumina GAII
2012-08-10 | E-GEOD-39308 | biostudies-arrayexpress
Project description:The lack of MIRNA set and genome sequence of O. rufipogon (the ancestor of the cultivated rice) has limited to answer the role of MIRNA genes in rice domestication.In this study, a genome, three small RNA populations and a degradome of O.rufipogon were sequenced by Illumina platform and miRNA expression were investigated by miRNA chips. A de novo genome was assembled using ~55x coverage of raw sequencing data and a total of 387 MIRNAs were identified in the O. rufipogon genome based on ~5.2 million unique small RNA reads from three different tissues of O. rufipogon. Of these O. rufipogon MIRNAs, 259 were not found in the cultivated rice, suggesting loss of these MIRNAs in the cultivated rice. We also found that 48 MIRNAs were novel in the cultivated rice, suggesting that they were potential targets of domestication selection. Some miRNAs showed significant expression difference in the wild and cultivated rice, suggesting that expression of miRNA could also be a target of domestication, as demonstrated for the miR164 family. Our results illustrated MIRNA genes, like protein-coding genes, were significantly shaped during rice domestication and could be one of the driven forces contributed to rice domestication.
2012-08-10 | GSE39307 | GEO