Light is one of the most important factors regulating plant gene expression patterns, metabolism, physiology, growth, and development. To explore how light may induce or alter transcript splicing, we ...conducted RNA-Seq-based transcriptome analyses by comparing the samples harvested as etiolated seedlings grown under continuous dark conditions vs. the light-treated green seedlings. The study aims to reveal differentially regulated protein-coding genes and novel long noncoding RNAs (lncRNAs), their light-induced alternative splicing, and their association with biological pathways. We identified 14,766 differentially expressed genes, of which 4369 genes showed alternative splicing. We observed that genes mapped to the plastid-localized methyl-erythritol-phosphate (MEP) pathway were light-upregulated compared to the cytosolic mevalonate (MVA) pathway genes. Many of these genes also undergo splicing. These pathways provide crucial metabolite precursors for the biosynthesis of secondary metabolic compounds needed for chloroplast biogenesis, the establishment of a successful photosynthetic apparatus, and photomorphogenesis. In the chromosome-wide survey of the light-induced transcriptome, we observed intron retention as the most predominant splicing event. In addition, we identified 1709 novel lncRNA transcripts in our transcriptome data. This study provides insights on light-regulated gene expression and alternative splicing in rice.
Abstract
Expression Atlas (http://www.ebi.ac.uk/gxa) is an added value database that provides information about gene and protein expression in different species and contexts, such as tissue, ...developmental stage, disease or cell type. The available public and controlled access data sets from different sources are curated and re-analysed using standardized, open source pipelines and made available for queries, download and visualization. As of August 2017, Expression Atlas holds data from 3,126 studies across 33 different species, including 731 from plants. Data from large-scale RNA sequencing studies including Blueprint, PCAWG, ENCODE, GTEx and HipSci can be visualized next to each other. In Expression Atlas, users can query genes or gene-sets of interest and explore their expression across or within species, tissues, developmental stages in a constitutive or differential context, representing the effects of diseases, conditions or experimental interventions. All processed data matrices are available for direct download in tab-delimited format or as R-data. In addition to the web interface, data sets can now be searched and downloaded through the Expression Atlas R package. Novel features and visualizations include the on-the-fly analysis of gene set overlaps and the option to view gene co-expression in experiments investigating constitutive gene expression across tissues or other conditions.
Abstract
The Planteome project (http://www.planteome.org) provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common ...standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. The reference ontologies include the Plant Ontology, Plant Trait Ontology and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and Attribute Ontology, and others. The project also provides access to species-specific Crop Ontologies developed by various plant breeding and research communities from around the world. We provide integrated data on plant traits, phenotypes, and gene function and expression from 95 plant taxa, annotated with reference ontology terms. The Planteome project is developing a plant gene annotation platform; Planteome Noctua, to facilitate community engagement. All the Planteome ontologies are publicly available and are maintained at the Planteome GitHub site (https://github.com/Planteome) for sharing, tracking revisions and new requests. The annotated data are freely accessible from the ontology browser (http://browser.planteome.org/amigo) and our data repository.
The availability of RNA-Seq method allows researchers to capture the spatial or temporal profile of transcriptomes from various types of biological samples. The transcriptome data from a species can ...be analyzed in the context of its sequenced genomes or closely related genome to score biological sample-specific transcript isoforms, novel transcribed regions and to refine gene models including identification of new genes, in addition to the differential gene expression analysis. However, many plant species of importance currently lack a sequenced genome or a closely related reference genome and thus, rely on the de novo methods for generating transcript models and transcriptome assemblies. Here we describe various tools used for de novo transcriptome assembly and discuss the data management practices and standards.
This paper outlines an experimental investigation into the durability of large-scale adhesively bonded joints with a thick layer of methyl methacrylate adhesive (MMA). Ageing has been performed by ...immersion in a 3.5 wt% NaCl solution for 10 weeks at 50°C. Two aged and one unaged specimen were subjected to tensile testing, and three aged and one unaged specimen were loaded up to ~ 3.5 million fatigue cycles followed by a residual tensile test. The ductility of the adhesive is affected by ageing and fatigue testing. Despite a decrease in ductility, the plastic zone development was adequate for the required strain redistribution without compromising the joint performance (strength and stiffness) demonstrating the fatigue tolerance of the joint. The shear, longitudinal, and peel strain values in the adhesive bulk are evaluated by digital image correlation. The shear strength values are significantly higher than the requirements following from the design. All specimens failed by sudden delamination of the composite plate. Post-mortem analysis showed no corrosion travel at the interface of steel and adhesive.
Abiotic stresses affect plant physiology, development, growth, and alter pre-mRNA splicing. Western poplar is a model woody tree and a potential bioenergy feedstock. To investigate the extent of ...stress-regulated alternative splicing (AS), we conducted an in-depth survey of leaf, root, and stem xylem transcriptomes under drought, salt, or temperature stress. Analysis of approximately one billion of genome-aligned RNA-Seq reads from tissue- or stress-specific libraries revealed over fifteen millions of novel splice junctions. Transcript models supported by both RNA-Seq and single molecule isoform sequencing (Iso-Seq) data revealed a broad array of novel stress- and/or tissue-specific isoforms. Analysis of Iso-Seq data also resulted in the discovery of 15,087 novel transcribed regions of which 164 show AS. Our findings demonstrate that abiotic stresses profoundly perturb transcript isoform profiles and trigger widespread intron retention (IR) events. Stress treatments often increased or decreased retention of specific introns - a phenomenon described here as differential intron retention (DIR). Many differentially retained introns were regulated in a stress- and/or tissue-specific manner. A subset of transcripts harboring super stress-responsive DIR events showed persisting fluctuations in the degree of IR across all treatments and tissue types. To investigate coordinated dynamics of intron-containing transcripts in the study we quantified absolute copy number of isoforms of two conserved transcription factors (TFs) using Droplet Digital PCR. This case study suggests that stress treatments can be associated with coordinated switches in relative ratios between fully spliced and intron-retaining isoforms and may play a role in adjusting transcriptome to abiotic stresses.
This work reports a study of the fatigue behaviour and quasi‐static strength of full‐scale adhesively bonded steel‐composite joints. Three joints with an approximately 10‐mm‐thick layer of methyl ...methacrylate adhesive were manufactured in dockyard conditions. One specimen was tensile tested till failure, while two specimens were subjected to ~3.5 million fatigue cycles, followed by a residual tensile test supported with digital image correlation. The shear, longitudinal and peel strain values within the adhesive bondlines are significantly higher at the gripped sides due to the asymmetrical design of the steel brackets. All specimens showed a significantly higher shear strength than the design values defined by the shipbuilder. Fibre Bragg sensors monitored strains at steel and composite constituents and allowed to detect damage onset and evolution in tensile tested specimens. A finite element model of the joint was developed with material and interface properties based on dedicated small‐scale experiments. The simulation results of strains during a static load test corresponded closely to the DIC measurements. All specimens failed near the composite‐adhesive interface due to delamination of the composite panel.
Gramene (http://www.gramene.org) is an online resource for comparative functional genomics in crops and model plant species. Its two main frameworks are genomes (collaboration with Ensembl Plants) ...and pathways (The Plant Reactome and archival BioCyc databases). Since our last NAR update, the database website adopted a new Drupal management platform. The genomes section features 39 fully assembled reference genomes that are integrated using ontology-based annotation and comparative analyses, and accessed through both visual and programmatic interfaces. Additional community data, such as genetic variation, expression and methylation, are also mapped for a subset of genomes. The Plant Reactome pathway portal (http://plantreactome.gramene.org) provides a reference resource for analyzing plant metabolic and regulatory pathways. In addition to ∼ 200 curated rice reference pathways, the portal hosts gene homology-based pathway projections for 33 plant species. Both the genome and pathway browsers interface with the EMBL-EBI's Expression Atlas to enable the projection of baseline and differential expression data from curated expression studies in plants. Gramene's archive website (http://archive.gramene.org) continues to provide previously reported resources on comparative maps, markers and QTL. To further aid our users, we have also introduced a live monthly educational webinar series and a Gramene YouTube channel carrying video tutorials.
This paper reports on the development of a methodology for evaluating the fatigue damage evolution in single and double lap adhesively bonded joints subjected to constant and variable fatigue ...loading. First, a methodology is developed to monitor the evolution of permanent deformation, stiffness degradation and hysteresis losses of single lap joints subjected to constant amplitude fatigue load. During the test, the global deformation of the adhesive joint is monitored using digital image correlation (DIC). A MATLAB code is developed to analyse and visualize the evolution in stiffness degradation and energy dissipation during the course of a complete fatigue test. Hereto ellipses are fitted to the hysteresis loops in the recorded load-deformation data. The slope of the main axis of the ellipse and its enclosed area are extracted to determine stiffness and dissipated energy, respectively. Next, the methodology is optimized for implementation during fatigue testing of double lap joints with different bond line thicknesses. The results of the experimental study reveal a distinct relation between stiffness degradation and increase in hysteresis losses with increasing number of fatigue cycles or thus increasing fatigue damage.
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