Project description:New RNA-seq data was generated to create a large-scale Seminavis robusta gene expression atlas profiling a wide-range of experimental conditions including life cycle stages and abiotic stressors. These stresses encompass among others changes in temperature and salt concentration, silica depletion, high light exposure, H202 and decadienal treatment.
Project description:Innate immune cells are a promising system for studying cell type evolution, as they are widespread across Metazoa, have several conserved functions, and are under selective pressure from pathogens. However, molecular characterizations of invertebrate immune cells are limited, and we do not know whether invertebrate immune cell types are homologous to those in vertebrates. Here we present a single-cell atlas of blood cells from a basal chordate, Ciona robusta, which lacks vertebrate innovations such as red blood cells and adaptive immunity. Using single-cell RNA sequencing, in situ hybridization, and live reporters, we extend definitions of C. robusta blood cells by showing that canonical, morphologically-defined cell types are transcriptomically heterogeneous. We find evidence that circulating blood contains a differentiation hierarchy with at least five major lineages. Mature blood cells include phagocytes, as well as over 20 cell states variously expressing vanadium-binding proteins, carbonic anhydrases, pattern recognition receptors, cytokines, and complement factors. Despite the expression of homologs to vertebrate immune components, we find that tunicate and vertebrate blood cell states share no clear homology in their transcriptomic profiles. Expression of transcription factors has also diverged. Altogether, this work modernizes blood cell classifications in C. robusta and reveals a surprising diversity of immune cells within chordates.
2025-05-23 | GSE296253 | GEO
Project description:Total genomic DNA sequencing of Azygia robusta
Project description:Analyses of new genomic, transcriptomic or proteomic data commonly result in trashing many unidentified data escaping the ‘canonical’ DNA-RNA-protein scheme. Testing systematic exchanges of nucleotides over long stretches produces inversed RNA pieces (here named “swinger” RNA) differing from their template DNA. These may explain some trashed data. Here analyses of genomic, transcriptomic and proteomic data of the pathogenic Tropheryma whipplei according to canonical genomic, transcriptomic and translational 'rules' resulted in trashing 58.9% of DNA, 37.7% RNA and about 85% of mass spectra (corresponding to peptides). In the trash, we found numerous DNA/RNA fragments compatible with “swinger” polymerization. Genomic sequences covered by «swinger» DNA and RNA are 3X more frequent than expected by chance and explained 12.4 and 20.8% of the rejected DNA and RNA sequences, respectively. As for peptides, several match with “swinger” RNAs, including some chimera, translated from both regular, and «swinger» transcripts, notably for ribosomal RNAs. Congruence of DNA, RNA and peptides resulting from the same swinging process suggest that systematic nucleotide exchanges increase coding potential, and may add to evolutionary diversification of bacterial populations.
Project description:Single-cell RNA sequencing (scRNA-seq) enables discovery of novel cell states by transcriptomic profiling with minimal prior knowledge, making it useful for studying non-model organisms. For most marine organisms, however, cells are viable at a higher salinity than is compatible with scRNA-seq, impacting data quality and cell representation. We show that a low-salinity phosphate buffer supplemented with D-mannitol (PBS-M) enables higher-quality scRNA-seq of blood cells from the tunicate Ciona robusta. Using PBS-M reduces cell death and ambient mRNA, revealing cell states not otherwise detected. This simple protocol modification could enable or improve scRNA-seq for the majority of marine organisms.
Project description:To study the floral volatile compounds of standard Malus robusta flowers (Mr), and its progeny with strongly and weakly fragrant flowers