Project description:The present dataset was applied to investigate the structural characterization of flavonoid-O-glycoconjugates using massive molecular networks embedding information based on chemical and taxonomical data (including previous findings on mechanistically and struc-turally gas-phase chemistry of flavonoids, plant species and metabolic distributions).
Project description:Nucleosomes that contain the histone variant H2A.Z are enriched around transcriptional start sites in many organisms. A single octameric nucleosome can contain two H2A.Z histones (homotypic) or one H2A.Z and one canonical H2A (heterotype). We generated high-resolution maps of homotypic and heterotypic Drosophila H2A.Z (H2Av) nucleosomes. Although homotypic and heterotypic H2Av nucleosomes map throughout most of the genome, homotypic nucleosomes are enriched and heterotypic nucleosomes are depleted downstream of active promoters and intron/exon boundaries. The distribution of homotypic H2A.Z nucleosomes resembles that of salt-soluble nucleosomes and shows evidence of displacement during transcriptional elongation. Homotypic nucleosomes are also depleted downstream of paused polymerases, where salt-soluble nucleosomes are conspicuously depleted. Our results suggest a model whereby H2A.Z enrichment patterns result from different structural interactions within the core of heterotypic and homotypic nucleosomes following disruption during transcriptional elongation. We analyzed two replicates for input, heterotypic and homotypic purifications. We sequenced one library for each of the single H2Av pulldown and 80mM salt soluble samples.
Project description:We conducted field surveys to detect the population density of the most important invasive weed species and their associated virus vectoring aphids in crops grown under high input (HIF) vs low-input (LIF) field conditions, with and without fertilizers and pesticides. The most frequent invasive weed species were Stenactis annua, Erigeron canadensis and Solidago canadensis. These species were hosts predominantly for the aphids Brachycaudus helichrysi and Aulacorthum solani in both management systems. The 13% higher coverage of S. annua under LIF conditions resulted in a 30% higher B. helichrysi abundance and ~85% higher A. solani abundance compared with HIF conditions. To reveal virus infection in crop plants and invasive weeds high-throughput sequencing of small RNAs were carried out. Bioinformatics analysis of the results detected the presence of 16 important plant viruses, but not resulting strikingly different pattern under LIF and HIF. This could suggest that invasive weeds serves as a virus reservoir both under low and high input management systems. The lake of any management increases virus vector aphids abundances, their presence has a great impact on the viromes of the crops.
Project description:This a reciprocal transplant experiment. Two hebivorous lepidoptera species (Ostrinia nubilalis and Ostrinia scapulalis) have been fed either their preferred plant (corn for O.nubilalis and Mugwort for O. scapulalis) or the reciprocal plant. At 4th larval instar, RNA was extracted from whole larvae, size selected to enrich in small RNAs and sequenced by Illumina single-end 50bp.
Project description:Asterids is one of the major plant clades comprising of many commercially important medicinal species. One of the major concerns in medicinal plant industry is adulteration/contamination resulting from misidentification of herbal plants. This study reports the construction and validation of a microarray capable of fingerprinting medicinally important species from the Asterids clade.
Project description:The transcriptional regulatory structure of plant genomes remains poorly defined relative to that of animals. It has been unclear how many cis-regulatory elements generally exist in plant genomes, where these elements lie in relation to their target promoters, and how these features are conserved across species. We employed the Assay for Transposase-Accessible Chromatin with sequencing (ATAC-seq) in four different plant species (Arabidopsis thaliana, Medicago truncatula, Solanum lycopersicum, and Oryza sativa) to delineate open chromatin regions and transcription factor (TF) binding sites across each genome. Despite a ~10-fold variation in intergenic space among species, the majority of open chromatin regions consistently lie within 3 kb upstream of a transcription start site (TSS) in all four species. Nearly 70% of genes in Arabidopsis, Medicago, and Rice have a single putative regulatory region upstream of the TSS, while a similar percentage of tomato genes have 2-5 such elements. Despite variation in the location and number of regulatory elements within orthologous gene sets, transcriptional regulatory networks appear to be largely conserved across species. Profiling of open chromatin in the Arabidopsis root hair and non-hair epidermal cell types indicated that while the open chromatin landscapes of these two cell types were largely indistinguishable on a global scale, thousands of relatively subtle, quantitative cell-specific differences could be found. Analysis of TF binding sites in these differentially accessible regions led to the discovery of a MYB-driven transcriptional regulatory module unique to the hair cell type, which appears to control both hair cell fate regulators and abiotic stress responses. Our cross-species and cross-cell type analyses revealed common transcriptional regulatory principles among species and shed light on the mechanisms that produce cell type-specific transcriptomes during development.
