Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1276249 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:This work represents the first epigenomic study carried out on saffron crocus. Five accessions of saffron, showing differences in tepal pigmentation, yield of saffron and flowering time, were analysed at the epigenetic level by applying a methylation-sensitive restriction enzyme-sequencing (MRE-seq) approach. Five accession-specific hypomethylomes plus a reference hypomethylome, generated by combining the sequence data from the single accessions, were obtained. Assembled sequences were annotated against existing online databases. In the absence of the Crocus genome, the rice genome was mainly used as the reference as it is the best annotated genome among monocot plants. Comparison of the hypomethylomes revealed many differentially methylated regions, confirming the high epigenetic variability present among saffron accessions, including sequences encoding for proteins that could be good candidates to explain the accessions’ alternative phenotypes. In particular, transcription factors involved in flowering process (MADS-box and TFL) and for the production of pigments (MYB) were detected. Finally, by comparing the generated sequences of the different accessions, a high number of SNPs, likely having arisen as a consequence of the prolonged vegetative propagation, were detected, demonstrating surprisingly high genetic variability. Gene ontology (GO) was performed to map and visualise sequence polymorphisms located within the GOs and to compare their distributions among different accessions. As well as suggesting the possible existence of alternative phenotypes with a genetic basis, a clear difference in polymorphic GO is present among accessions based on their geographic origin, supporting a possible signature of selection in the Indian accession with respect to the Spanish ones.
2021-03-24 | GSE166350 | GEO
Project description:Low temperature is one of the major abiotic stresses limiting rice growth and productivity, it is urgent to reveal the genetic and molecular mechanisms of plant responses to low temperature stress and to search for useful genetic resources for improving low-temperature tolerance. the 8 accessions from China Core Collection include 4 cold tolerance accessions, 3 sensitivity accessions and 1 intermediate type accession. We used microarrays to detail variation of the gene expression after cold treatment and screen more cold-response genes in rice.
2015-10-01 | GSE71680 | GEO
Project description:Annelid mitochondrial genes newly assembled from SRA data
| PRJDB14830 | ENA
Project description:Genomic diversity is a source of transcriptomic and phenotypic diversities. Although genomic variations in rice (Oryza sativa) accessions have been extensively analyzed, information of transcriptomic and phenotypic variations, especially for below-ground variations, are limited. Here, we report the diversities of above- and below-ground traits and transcriptomes in highly diversified 61 rice accessions grown in the upland-field. We found that phenotypic variations were explained by four principal components and that tiller numbers and crown root diameters could summarize admixture groups. Transcriptome analysis revealed that admixture-group-associated differentially expressed genes were enriched with stress response related genes, suggesting that admixture groups have distinct stress response mechanisms. Root growth was negatively correlated with auxin inducible genes, suggesting the association between auxin signaling and mild drought stress. Negative correlation between crown root diameters and stress response related genes suggested that thicker crown root diameter is associated with mild drought stress tolerance. Finally co-expression network analysis implemented with DAP-seq analysis identified phytohormone signaling network and key transcription factors negatively regulating crown root diameters. Our datasets would serve as an important resource for understanding genomic and transcriptomic basis of phenotypic variations under the upland-field condition.
2021-03-07 | GSE162312 | GEO
Project description:10 DeNovo assembled rice genomes
| PRJEB51974 | ENA
Project description:Twenty-four nucleotide long miRNAs (lmiRNAs) direct DNA methylation at target genes and regulate their transcription. The evolutionary origin of lmiRNAs and the range of lmiRNA-mediated regulation remain obscure. Here, we reannotated lmiRNAs and their targets in rice by applying stringent criteria. We found that the majority of lmiRNAs are derived from MITEs and most sites targeted by MITE-derived lmiRNAs reside within MITEs, suggesting co-evolution of lmiRNAs and their targets through MITE amplification. lmiRNAs undergo dynamically changes under stressed conditions and the genes targeted by lmiRNAs show an enrichment for stress responsive genes, suggesting that lmiRNAs are widely involved in plant response to stresses. We constructed the evolutionary histories of lmiRNAs and their targets. lmiRNAs emerged before or when the AA genome was diverged, while the emergence of lmiRNA targets coincided with or followed the emergence of lmiRNAs. Furthermore, we found that the sequences of a lmiRNA target site underwent variations, coincident with the divergence of rice accessions and the distribution of rice accessions in different geographical locations and climatic conditions. Our findings highlight MITEs as an important origin of lmiRNAs and suggest that the evolution of lmiRNA-target regulatory modules may contribute to rice adaptation to environmental changes.
2023-11-01 | GSE217602 | GEO
Project description:Salinity is a major constraint on agricultural productivity worldwide. Despite the serious impacts of salinity on rice yields, particularly in Asia, mechanisms of salt tolerance in wild rice species are yet to be explored. Here we extracted and quantified root microsomal proteins of Oryza australiensis accessions contrasting in salt tolerance. Whole root systems of two-week-old seedlings were treated with 80 mM NaCl for 30 days or left untreated. Proteins were quantified by tandem mass tags (TMT) and triple-stage MS. We found >200 differentially expressed proteins (DEPs) between the salt-treated and control in the two accessions (p-value <0.05). Gene Ontology (GO) analysis showed that ‘metabolic process’, ‘transport’ and ‘transmembrane transporter’ activities were highly responsive categories following salt treatment of the O. australiensis seedlings. In particular, ATPases and SNARE proteins were up-regulated in the salt-tolerant accession and appeared to have a major role in response to salinity. ATPases are the central link between energy generation and transport, while SNARE proteins facilitate vesicle fusion and interact with voltage-gated potassium channels to regulate K+ influx. We successfully validated the putative function of two strongly upregulated proteins, a monosaccharide transporter and a VAMP-like protein, by measuring the growth under salinity of yeast mutants in which homologous genes were deleted. Our results demonstrate the potential use of wild species as a source of new mechanisms of salt tolerance for the breeding of elite cultivars of rice.
2019-09-11 | PXD013701 | Pride
Project description:To identify genes that co-express with rice cellulose synthase genes involved in rice secondary cell wall formation, transcriptome analyses was performed using rice internodesbefore and after the heading stage, where secondary cell wall formation extensively occur. Transcriptomes of rice third or the fourth internodes were analyzed at 17, 8, and 1 day before, and 6, 13, and 35 days after heading Please note that the current data were normalized together with additional 143 sample data available in GEO and the list of the sample accessions is provided in Series supplementary file [normalized_together_GSMs.txt].
2013-10-01 | E-GEOD-51289 | 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 | GSE39308 | GEO