Project description:Invasive plants can significantly disrupt native biodiversity, yet the genetic mechanisms driving their success remain poorly understood. This study investigates the genetic basis of invasiveness in the common reed (Phragmites australis), a resilient grass species that became invasive in North America following its introduction from Europe. By integrating whole-genome sequencing with bulk, single-cell, and spatial transcriptomics, we constructed a comprehensive single-cell atlas of the common reed's shoot system. UMAP analysis revealed 19 distinct cell clusters within the shoot, which were annotated using Gene Ontology (GO) enrichment to identify key cell types, including mesophyll, epidermal, bundle sheath, differentiating vascular cells, shoot apical meristems, and a cell cycle-associated cluster. We inferred key genes involved in the specification of several tissues, such as epidermal cells and ground meristems. For gene expression analysis, shoot tissues from three individuals of the invasive North American population and three from the native European population were included. Comparative transcriptomic analysis revealed significant upregulation of genes associated with the light-harvesting components of photosynthesis in several tissues of the invasive population, while genes involved in the respiratory burst related to defense responses were notably downregulated.
Project description:The Human Induced Pluripotent Stem Cells Initiative (HipSci) project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national induced pluripotent stem cell (iPS cell) resource and use it to carry out cellular genetic studies. In this sub-study we performed Expression analysis using the using RNAseq of fibroblasts, peripheral blood mononuclear cells (PBMCs) and induced pluripotent stem cells (iPS cells) generated from the skin biopsies or blood of healthy volunteers. This experiment includes the data and expands the metadata from two obsolete ArrayExpress accessions (E-ERAD-216 and E-ERAD-327) for use in the Expression Atlas. For samples derived from E-ERAD-216 the raw data is stored in the European Genome-Phenome Archive (EGA) and is subject to access control. Data from E-ERAD-327 is stored in the European Nucleotide Archive (ENA) and is publicly available.