Tissue and developmental atlas of Brachypodium distachyon
Ontology highlight
ABSTRACT: Due to its small and sequenced genome, short generation time, efficient transformation and increasing genetic resources, Brachypodium distachyon is an emerging model for grasses. Despite this, data capturing gene expression patterns across different organs and developmental stages is missing. We have generated a comprehensive gene expression atlas for Brachypodium, capturing 9 different organs and developmental stages
Project description:In tomato, there are seven ethylene receptors, ETR1, ETR2, ETR3, ETR4, ETR5, ETR6, and ETR7. In our laboratory, we have ETR3, ETR4, and ETR7, loss-of-function single mutants, in this study we compare the pollen tube length of ETR mutant KO with WT and NR (never rip) gain of function mutant. We found the pollen tube length in ETR3, ETR4, and ETR7 (KO) was more than WT; on the other hand, NR was less than WT, and the treatment by ethylene (ET) increase the length of pollen tube in all ETRs KO and WT but not in NR. The treatment by MCP-1 decreases the pollen tube length slightly in WT, 20% in ETR (KO) and no effect in NR. In conclusion, our results suggest that ethylene receptors (ETRs) in the active state inhibit pollen tube growth; therefore the ethylene is an essential factor for male gametophyte growth.
Project description:The goal of this study was to examine the transcriptional events occuring during stress-free Brachypodium distachyon root development via illumina paired-end RNA-seq. 4 time-points were chosen that capture the transition from rapid vegetative growth into slower reproductive growth. Abstract - Root systems are dynamic, adaptable organs that play critical roles in plant development. Roots, however, remain understudied and therefore present opportunities for trait improvement in food and bioenergy crops. A comprehensive growth stage-based root phenotyping integrated with molecular signatures is required to advance our understanding of root growth and development. Here we studied Brachypodium distachyon rooting process by monitoring root biomass, length, branching, root-to-shoot ratio and Carbon-to-Nitrogen ratio during time. To provide insight into gene regulation that accompanies root development and biomass accumulation, we generated comprehensive transcript profiles of Brachypodium whole-root system at four initial developmental stages that capture the transition from vegetative to reproductive growth. Our stringent data analysis revealed that multiple biological processes and various families of transcription factors (TFs) were differentially expressed during root development. In particular, the AUX/IAA, ERFs, WRKY, NAC, and MADS TF family members were upregulated, while ARFs and GRFs were downregulated in a time-dependent manner. Our results suggested particular TF families and biological processes including trehalose metabolism as important factors possibly involved in root biomass accumulation. We introduced several Brachypodium root biomass-promoting genes which can be employed by the genome editing approaches for improving biomass productivity in grasses.
Project description:Background: Since the proposal of Brachypodium distachyon as a model for the grasses over 500 Bdi-miRNAs have been annotated in miRBase making Brachypodium second in number only to rice. Other monocots, such as switchgrass, are completely absent from the miRBase database. While a significant number of miRNAs have been identified which are highly conserved across plants, little research has been done with respect to the conservation of miRNA targets. Plant responses to abiotic stresses are regulated by diverse pathways many of which involve miRNAs; however, it can be difficult to identify miRNA guided gene regulation when the miRNA is not the primary regulator of the target mRNA. Results: To investigate miRNA target conservation and stress response involvement, a set of PARE (Parallel Analysis of RNA Ends) libraries totaling over 2 billion reads was constructed and sequenced from Brachypodium, switchgrass, and sorghum representing the first public release of degradome data from the latter two species. Analysis of this data provided not only PARE evidence for miRNA guided cleavage of over 7,000 predicted target mRNAs in Brachypodium, but also evidence for miRNA guided cleavage of over 1,000 homologous transcripts in sorghum and switchgrass. A pipeline was constructed to compare RNA-seq and PARE data made from Brachypodium plants exposed to various abiotic stress conditions. This resulted in the identification of 44 miRNA targets which exhibit stress regulated cleavage. Time course experiments were performed to reveal the relationship between miR393ab, miR169a, miR394ab, and their respective targets throughout the first 36 hours of the cold stress response in Brachypodium. Conclusions: Knowledge gained from this study provides considerable insight into the degradomes and the breadth of miRNA target conservation among these three species. Additionally associations of a number of miRNAs and target mRNAs with the stress responses have been revealed which will aid researchers in developing stress tolerant transgenic crops.
Project description:Some microorganisms can respire with extracellular electron acceptors using an extended electron transport chain to the cell surface. These organisms apply flavin molecules as cofactors to facilitate one-electron transfer catalysed by the terminal reductases and as endogenous electron shuttles. In the model organism Shewanella oneidensis, riboflavin production and excretion triggers a specific biofilm formation response that is initiated at a specific threshold concentration, similar to canonical quorum sensing molecules. Riboflavin-mediated messaging is based on the overexpression of the gene encoding the putrescin decarboxylase speC which leads to posttranscriptional overproduction of proteins involved in biofilm formation. We performed a mass spectrometry-based analysis of cells with and without speC overexpression to identify the effect of SpeC overexpression on the cell proteome.
Project description:Using comparative genomic hybridization we examined the genome content of 30 isolates of E. coli and Shigella to determine the relative location of E. coli isolates from the human neobladder Isolates were included in the study that represent the prototype strains of multiple pathovars. No replicates were included in the final comparisons
Project description:The Poaceae family, also known as the grasses, includes agronomically important cereal crops such as rice, maize, sorghum, and wheat. Previous comparative studies have shown that much of the gene content is shared among the grasses; however, functional conservation of orthologous genes has yet to be explored. To gain an understanding of the genome-wide patterns of evolution of gene expression across reproductive tissues, we employed a sequence-based approach to compare analogous transcriptomes in species representing three Poaceae subgroups including the Pooideae (Brachypodium distachyon), the Panicoideae (sorghum), and the Ehrhartoideae (rice). Our transcriptome analyses reveal that only a fraction of orthologous genes exhibit conserved expression patterns. A high proportion of conserved orthologs include genes that are upregulated in physiologically similar tissues such as leaves, anther, pistil, and embryo, while orthologs that are highly expressed in seeds show the most diverged expression patterns. This experiment is related to E-MTAB-4401 (http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-4401/) and E-MTAB-4402 (http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-4402/)
Project description:The Poaceae family, also known as the grasses, includes agronomically important cereal crops such as rice, maize, sorghum, and wheat. Previous comparative studies have shown that much of the gene content is shared among the grasses; however, functional conservation of orthologous genes has yet to be explored. To gain an understanding of the genome-wide patterns of evolution of gene expression across reproductive tissues, we employed a sequence-based approach to compare analogous transcriptomes in species representing three Poaceae subgroups including the Pooideae (Brachypodium distachyon), the Panicoideae (sorghum), and the Ehrhartoideae (rice). Our transcriptome analyses reveal that only a fraction of orthologous genes exhibit conserved expression patterns. A high proportion of conserved orthologs include genes that are upregulated in physiologically similar tissues such as leaves, anther, pistil, and embryo, while orthologs that are highly expressed in seeds show the most diverged expression patterns. This experiment is related to E-MTAB-4400 (http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-4400/) and E-MTAB-4402 (http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-4402/)
Project description:Monocot grass species (Poaceae) express a diverse set of multisubunit RNA polymerase enzymes, including Pol II, Pol IV and Pol V. To better understand this functional diversity, we have charted Pol IV function in the model Brachypodium distachyon. Intriguingly, pol IV null mutations in Poaceae crops disrupt growth, reproductive development and seed set. In order to investigate how Pol IV controls vegetative growth and TE activity in these grasses, we have isolated B. distachyon mutant alleles for Pol IV’s largest subunit, NRPD1. We obtained the germplasm in which to screen for these pol IV mutations from the B. distachyon community's sodium azide (NaN) and T-DNA insertion collections.
Project description:Brachypodium, also called as Purple False Brome, a bioenergy crop model is related to grasses and major cereal grain species especially Triticeae (wheat, barley, etc.). It's small genome size, a short life cycle, and few growth requirements make this plant as a model for functional genomics studies. At the time of germination, the exposure to light may play an important role in the early development of the seedling. In order to explore transcriptional programs and genes operating in dark and light conditions, an RNA-Seq based study of 6 libraries prepared from poly-A rich mRNA fraction was carried out. For each treatment type dark and light, three individual plants were used as biological replicates.
Project description:EXOSC10 is a catalytic subunit of the nuclear RNA exosome with an exoribonuclease activity. The enzyme processes and degrades different classes of RNAs. To delineate the role of EXOSC10 during oocyte growth, specific Exosc10 inactivation was performed in the oocytes from the primordial follicle stage onward using the Gdf9-iCre; Exosc10f/- mouse model (Exosc10cKO(Gdf9)). Exosc10cKO(Gdf9) female mice are infertile. The onset of puberty and the estrus cycle in mutants are initially normal and ovaries contain all follicle classes. By the age of eight weeks, vaginal smears reveal irregular estrus cycles and mutant ovaries display a complete depletion of follicles. Mutant oocytes retrieved from the oviduct are degenerated, sometimes showing an enlarged polar body which may reflect a defective first meiotic division. Under fertilization conditions, the mutant oocytes do not enter into an embryonic development process. Furthermore, we conducted a comparative proteome analysis of wild type and Exosc10 knockout mouse ovaries and identified EXOSC10-dependent proteins involved in many biological processes, such as meiotic cell cycle progression and oocyte maturation. Our results unambiguously demonstrate an essential role for EXOSC10 in oogenesis and may serve as a model for primary ovarian insufficiency in humans.