Ontology highlight
ABSTRACT:
PROVIDER: PRJNA438699 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:This study’s objective was to elucidate plant modifications and crown-specific transcriptome re-modeling that takes place in gibberellin-deficient barley sdw1 NILs exposed to increased temperatures. Experiments were designed to determine whether the phenotypic expression of sdw1 mutants is influenced by the allele-specific expression of the HvGA20ox2 gene or by wider genetic background variance and environmental cues. To achieve this goal, plants were examined considering phenotypic properties, physiological responses, and genomic constitution using high-throughput genotyping and sdw1 gene sequencing. We also employed the mRNA-seq method to acquire transcriptome-wide characterization of the crown tissue and provide new insights into the expression profiles of heat- and gibberellin-related genes.
2022-04-05 | E-MTAB-10789 | biostudies-arrayexpress
Project description:A greenhouse experiment was conducted at the Federal University of Alagoas in Maceio, Brazil. One-eye sett of sugarcane was planted in 20 liters plant pots, arranged in a completely randomized design and cultivated for 5 months before water privation.
2020-12-15 | GSE125069 | GEO
Project description:Cultivated soybean has domesticated in China for a long history, and there are several significant phenotypic differences between wild and cultivated soybeans. Seed of cultivar is generally larger than wild soybean, therefore here we comprehensively analyzed transcriptomes of thirteen soybean accessions seeds including seven wild soybeans and six landraces through applying strand-specific RNA sequencing. Differential expressed genes related seed weight were identified, some of them were known to be associated with seed development in Arabidopsis. Noncoding RNAs are known to play important roles in plant development, and we profiled the expression pattern of long noncoding RNA (lncRNA) in cultivated and wild soybean seeds. We have identified 1,251 long intergenic noncoding RNA, 243 intronic RNA and 81 antisense lncRNA, transcriptional levels of a number of lncRNAs were significantly different between cultivated and wild soybeans, suggesting that lncRNA may be involved in soybean seed development.
2017-06-13 | GSE94366 | GEO
Project description:Improving the yield by modifying plant architecture is key to progressive crop domestication. Here, we show that a 110-kb deletion on the short arm of chromosome 7 promotes the critical transition from semi-prostrate growth and low yield in wild rice (Oryza rufipogon), to erect growth and high yield in Asian cultivated rice (O. sativa). The microdeletion harbors a tandem repeat of seven putative Cys2-His2 zinc-finger genes. Three of these genes regulate the plant architecture in O. rufipogon and are closely linked to the previously identified PROSTRATE GROWTH 1 (PROG1) gene. Therefore, we refer to this locus as RICE PLANT ARCHITECTURE DOMESTICATION (RPAD). Furthermore, a similar but independent 113-kb deletion was detected at the RPAD locus in African cultivated rice. These results indicate that the deletions, coupled with the loss of a tandem repeat of zinc-finger genes, drove the parallel domestication of plant architecture in Asian and African rice.
2018-07-04 | GSE116423 | GEO
Project description:As the number of bacterial genomes and transcriptomes increases, so does the number of newly identified toxin–antitoxin (TA) systems. However, their functional characterization remains challenging, often requiring the use of overexpression vectors that can lead to misinterpretations. To fill this gap, we developed a systematic approach called FASTBAC-Seq (Functional AnalysiS of Toxin–Antitoxin Systems in BACteria by Deep Sequencing). Combining life/death phenotypic selection with next-generation sequencing, FASTBAC-Seq allows the rapid identification of loss-of- function (toxicity) mutations in toxin-encoding genes belonging to TA loci with nucleotide resolution. Here, we apply this new tool to study aapA3/IsoA3, a member of a new family of type I TA systems hosted on the chromosome of the major human gastric pathogen Helicobacter pylori.
2019-08-30 | GSE121423 | GEO
Project description:Phytochrome B (phyB), one member of phytochrome family in rice, plays important roles in regulating a range of developmental processes, and stress responses. However, little information about the mechanism involved in phyB-mediated light signaling pathway has been reported in rice. Another, it has been well-known that microRNAs (miRNAs) perform important roles in plant development and stress responses. Thus it is intriguing to explore the role of miRNAs in phyB-mediated light signaling pathway in rice. In this study, comparative high-throughput sequencing and degradome analysis were adopted to identify candidate miRNAs and their targets that participate in phyB-mediated light signaling pathway. A total of 838 known miRNAs, 663 novel miRNAs and 1,957 target genes were identified from wild-type (WT) and phyB mutant. Among them, 135 miRNAs showed differential expression, suggesting that the expressions of these miRNAs are under the control of phyB. In addition, 32 out of the 135 differentially expressed miRNAs were detected to slice 70 genes in rice genome. Analysis of these target genes showed that members of various transcription factor families constitute the largest proportion, indicating miRNAs are probably involved in phyB-mediated light signaling pathway mainly via regulating the expression of transcription factors. This study presented a comprehensive expression analysis of miRNAs and their targets that might be involved in phyB-mediated light signaling pathway for the first time. The results provide new clues for functional characterization of miRNAs in phyB-mediated light signaling pathway, which would be helpful in comprehensively uncovering molecular mechanism of phytochrome-mediated photomorphogenesis and stress responses in plant. Examination of miRNA profiles in wild type (WT) and phyB mutant at four-leaf stage by deep sequencing using Illumina Hiseq2500.
2015-01-01 | E-GEOD-62334 | biostudies-arrayexpress
Project description:Stochastic changes in cytosine methylation are a source of heritable epigenetic and phenotypic diversity in plants. Using the model plant Arabidopsis thaliana, we derive robust estimates of the rate at which methylation is spontaneously gained (forward epimutation) or lost (backward epimutation) at individual cytosines and construct a comprehensive picture of the epimutation landscape in this species. We demonstrate that the dynamic interplay between forward and backward epimutations is modulated by genomic context and show that subtle contextual differences have profoundly shaped patterns of methylation diversity in A. thaliana natural populations over evolutionary timescales. Theoretical arguments indicate that the epimutation rates reported here are high enough to rapidly uncouple genetic from epigenetic variation, but low enough for new epialleles to sustain long-term selection responses. Our results provide new insights into methylome evolution and its population-level consequences. MethylC-seq of Arabidopsis thaliana
2015-05-13 | E-GEOD-64463 | biostudies-arrayexpress
Project description:Food safety evaluation of new, genetically modified (GM) plant varieties has led to basic questions regarding the safety assessment of new plant varieties and whole foods derived thereof. An important part of the hazard identification in the European approach is a targeted compositional analysis of new GM plant varieties compared to one or more conventional reference varieties. Comparative analysis will become much more informative with unbiased analytical approaches, such as omics profiling. Analysis tools that estimate the similarity of new varieties to the reference would in turn greatly facilitate hazard identification. Further in-depth biological, functional and eventually toxicological analysis of the data would then only be necessary for varieties that fall outside the scale of those with a history of safe human consumption. For this purpose, the use of a one-class classifier tool was explored in this study to assess and classify transcriptome profiles of potato varieties. Five potato varieties were grown in the Netherlands during the same year (NL samples) and included four biological replicates for four varieties or two biological replicates for the fifth one. They were all analysed in 2011. A sixth variety was grown in the UK in a previous study and a previous year, for which the data are submitted in E-MTAB-605. The two UK samples were analysed in the original study in 2008 and again together with the NL samples in the present study, resulting in four profiles for two samples.
2014-03-04 | E-MTAB-1707 | biostudies-arrayexpress
Project description:The aim of the study was the elucidation of drought-induced molecular events related to plant hormones occurring in crown tissue of barley, the key organ for cereal survival. Experiments involving large-scale measurements of gene expression at transcript and protein level, hormone abundance, and phenotypic variability in a set of selected barley mutants were carried out to uncover how disturbance of GAs, BRs and SLs homeostasis may affect the barley multivariate response to drought. The characterization included early stages of plant development and continued to the later stages, with observation of effects on the whole-plant architecture and yield formation. The integration of all data allowed to enrich the knowledge of regulatory networks in barley exposed to drought.
2023-10-10 | E-MTAB-13358 | biostudies-arrayexpress
Project description:This research identifies a novel protein required for paramutation at the maize purple plant1 locus. This 'required to maintain repression2' (RMR2) protein represents the founding member of a plant-specific clade of hypothetical proteins. We show that RMR2 is required for transcriptional repression at the Pl1-Rhoades haplotype, for accumulation of 24 nt RNA species, and for maintenance of a 5-methylcytosine pattern distinct from that maintained by RNA polymerase IV. Genetic tests indicate that RMR2 is not required for paramutation occurring at the red1 locus. These results distinguish the paramutation-type mechanisms operating at specific haplotypes. The RMR2 clade of proteins provides a new entry point for understanding the diversity of epigenomic control operating in higher plants.
2012-04-16 | GSE37204 | GEO