Genome-wide analysis rice transcriptional change during the early stages of false smut formation caused by Ustilaginoidea virens
Ontology highlight
ABSTRACT:
ORGANISM(S): Oryza sativa Indica Group
SUBMITTER: Chao Quan
PROVIDER: E-GEOD-39049 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Rice false smut is a common fungal disease caused by Ustilaginoidea virens. As it only scatter occured in panicle at florescence, little information is known about this crop disease. Here, we injected suspension spores into a susceptible indica rice cultivar 9311 booting panicle (infected water as mock) and divided the early disease symptom into 3 uninterrupted stages(S) at 6 day post inoculation (dpi): the infected pistil became expand (S1), the hyphae began to infect the bottom of anthers (S2) and the hyphae growth went on and surrounded the floral organ forming a floral-hyphae complex (S3). To gain insight into rice putatively differential responses to U. virens, all 3 infected and mock spikes with same spike length were collected and analyzed by Solexa/IlluminaM-CM-"M-BM-^@M-BM-^Ys digital gene expression (DGE) system, BGI. Our results contribute to the knowledge of understanding rice molecular mechanism in response to U. virens infection. Four samples including one control (CK) and three infected (S1, S2, S3) were analyzed
2013-11-14 | E-GEOD-32010 | biostudies-arrayexpress
Project description:Rice false smut is a common fungal disease caused by Ustilaginoidea virens. As it only scatter occured in panicle at florescence, little information is known about this crop disease. In the previous study, 3 uninterrupted infecting stages were divided and each stage was monitored by Solexa/Illumina’s digital gene expression (DGE) system, and all data were submitted to NCBI (GSE32010). As the disease was greatly affected by environment and to eliminate environment factor, an experimental replication was done in 2011. Samples collection and analysis were described in GSE32010. Our results contribute to the knowledge of understanding rice molecular mechanism in response to U. virens infection. Four samples including one control (CK) and three infected (S1, S2, S3) were analyzed.
2013-11-14 | E-GEOD-39048 | biostudies-arrayexpress
Project description:Background: Vicia sativa (the common vetch) possesses a predominant zygomorphic flower and belongs to the subfamily Papilionoideae, which is related to Arabidopsis thaliana in the eurosid II clade of the core eudicots. Each vetch flower consists of 21 concentrically arranged organs: the outermost five sepals, then five petals and ten stamens, and a single carpel in the center. Methodology/Principal Findings: We explored the floral transcriptome to examine a genome-scale genetic model of the zygomorphic flower of vetch. mRNA was obtained from an equal mixture of six floral organs, leaves and roots. De novo assembly of the vetch transcriptome using Illumina paired-end technology produced 71,553 unigenes with an average length of 511 bp. We then compared the expression changes in the 71,553 unigenes in the eight independent organs through RNA-Seq Quantification analysis. We predominantly analyzed gene expression patterns specific to each floral organ and combinations of floral organs that corresponded to the traditional ABC model domains. Comparative analyses were performed in the floral transcriptomes of vetch and Arabidopsis, and genomes of vetch and Medicago truncatula. Conclusions/Significance: Our comparative analysis of vetch and Arabidopsis showed that the vetch flowers conform to a strict ABC model. We analyzed the evolution and expression of the TCP gene family in vetch at a whole-genome level, and several unigenes specific to three different vetch petals, which might offer some clues toward elucidating the molecular mechanisms underlying floral zygomorphy. Our results provide the first insights into the genome-scale molecular regulatory network that controls the evolution and development of the zygomorphic flower in Papilionoideae. Examination of the transcriptomic changes in the six floral organs, leaves and roots in common vetch.
2013-03-26 | E-GEOD-35437 | biostudies-arrayexpress
Project description:We reported the transcriptional profiles of E.coli expressing antimicrobial peptide LL37 under stress response condition. 4 samples, two groups, one group is under aerobic condition, the other group is under anaerobic condition. One of samples is E.coli which expressed LL37 as induction in each group, another sample is E.coli with no LL37 expression in vivo as control in each group.
2013-08-21 | E-GEOD-43408 | biostudies-arrayexpress
Project description:Background: Microorganisms are the major cause of food spoilage during storage, processing and distribution. Pseudomonas fluorescens is a typical spoilage bacterium that contributes to a large extent to the spoilage process of proteinaceous food. RpoS is considered an important global regulator involved in stress survival and virulence in many pathogens. Our previous work revealed that RpoS contributed to the spoilage activities of P. fluorescens by regulating resistance to different stress conditions, extracellular acylated homoserine lactone (AHL) levels, extracellular protease and total volatile basic nitrogen (TVB-N) production. However, RpoS-dependent genes in P. fluorescens remained undefined. Results: RNA-seq transcriptomics analysis combined with quantitative proteomics analysis basing on multiplexed isobaric tandem mass tag (TMT) labeling was performed for the P. fluorescens wild-type strain UK4 and its derivative carrying a rpoS mutation. A total of 375 differentially expressed genes (DEGs) and 212 differentially expressed proteins (DEPs) were identified in these two backgrounds. The DGEs were further verified by qRT-PCR tests, and the genes directly regulated by RpoS were confirmed by 5’-RACE-PCR sequencing. The combining transcriptome and proteome analysis revealed a role of this regulator in several cellular processes, including polysaccharide metabolism, intracellular secretion and extracellular structures, cell well biogenesis, stress responses, ammonia and biogenic amine production, which may contribute to biofilm formation, stress resistance and spoilage activities of P. fluorescens. Moreover, in this work we indeed observed that RpoS contributed to the production of the macrocolony biofilm’s matrix.
2019-11-12 | PXD010845 | Pride
Project description:RNA-Seq was performed to study the change of gene expression before and after cold treatment in Brachypodium. Different change patterns were identified. We have provided a complete view of transcriptome under cold stress condition, which will deepen our understanding of gene expression regulation in cold stress response as well as cold stress response mechanism for monocot plants. The mRNA profiles of 12-day-old Brachypodium seedlings with and without cold treatment (4 M-BM-0C for 24 h) were generated by deep sequencing using Illumina HiSeqM-bM-^DM-" 2000.
2013-07-15 | E-GEOD-48040 | biostudies-arrayexpress
Project description:According to the physiological change of the ear leaf, the developing ear leaf after pollination can be divided into three classes: mature leaves [ML, 0–14 days after pollination (DAP)]; early senescent leaves (ESL, 15–24 DAP); and later senescent leaves (LSL, 25–30 DAP). We harvested ear leaves at 12 DAP, 20 DAP, and 28 DAP, representing ML, ESL, and LSL, respectively. To identify genes involved in the leaf senescence process, we sequenced three cDNA libraries, ML (12 DAP), ESL (20 DAP), and LSL (28 DAP) using an Illumina HiSeqTM 2000.
2015-01-15 | E-MTAB-1709 | biostudies-arrayexpress
Project description:The anterior pituitary is the most important endocrine organ modulating animal postnatal growth, mainly by controlling growth hormone (GH) gene transcription, synthesis, and secretion. As an ideal model for animal postnatal growth studies, the Bama minipig is characterized as having a lower growth performance and fewer individual differences compared with larger pig breeds. In this study, anterior pituitaries from Bama minipig and Landrace pig were used for miRNA and mRNA expression profile analysis using miRNA microarrays and mRNA-seq. Consequently, a total of 222 miRNAs and 12,909 transcripts were detected, and both miRNAs and mRNAs in the two breeds showed high correlation (r > 0.97). Additionally, 41 differentially expressed miRNAs and 2,254 transcripts were identified. Pathways analysis indicated that 32 pathways significantly differed in the two breeds. Importantly, two GH-regulation-signalling pathways, cAMP and inositol 1, 4, 5-triphosphate (IP3), and multiple GH-secretion-related transcripts were significantly down-regulated in Bama minipigs. Moreover, target prediction by two algorithms (TargetScan and RNAhybrid) indicated that most miRNA–mRNA target pairs (63.68–71.33%) presented a negatively correlated expression pattern. A possible network among miRNAs, mRNAs, and GH-regulation pathways was also proposed. These data will be helpful in understanding the possible molecular mechanisms involved in animal postnatal growth. mRNA profiling in the anterior pituitary from two different pig breeds.2 pooled samples were analyzed. A pool of 3 pig anterior pituitary was used for Bama minpigs(YB) and Landrace pigs(YC),respectively.
2015-05-05 | E-GEOD-68490 | biostudies-arrayexpress
Project description:Corticosteroid use has epidemiologically been associated with invasive aspergillosis. We found that hydrocortisone and MP in physiological concentrations cause a change in morphology of A. fumigatus 293 growth with a less dense core, and straighter outgrowth of longer hyphae. Treated with MP, we found a differential expression of genes annotated to cell wall structure, and to cell cycle programme compared to untreated control, which could explain the changes in morphology. The up-regulation of genes encoding for toxins, iron acquisition, and cell wall components enforcing oxidative stress resistance would theoretically result in a more pathogenic A. fumigatus phenotype. Upregulation of pathways involved in DNA-repair might indicate on genotoxic effects of MP. Examination of test setting with 0.5 microM methylprednisolone versus control setting without methylprednisolone. Identification of differentially expressed genes (DEGs) was performed on the pooled data of the 3 samples treated with MP versus the 3 untreated control samples, with correction for the total number of reads per group.
2014-05-01 | E-GEOD-46559 | biostudies-arrayexpress
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2013-06-20 | E-GEOD-48156 | biostudies-arrayexpress