title: A first glimpse at the transcriptome of Physarum polycephalum.
abstract: BACKGROUND
  Physarum polycephalum, an acellular plasmodial species belongs to the amoebozoa, a major branch in eukaryote evolution. Its complex life cycle and rich cell biology is reflected in more than 2500 publications on various aspects of its biochemistry, developmental biology, cytoskeleton, and cell motility. It now can be genetically manipulated, opening up the possibility of targeted functional analysis in this organism.
  
  
  METHODS
  Here we describe a large fraction of the transcribed genes by sequencing a cDNA library from the plasmodial stage of the developmental cycle.
  
  
  RESULTS
  In addition to the genes for the basic metabolism we found an unexpected large number of genes involved in sophisticated signaling networks and identified potential receptors for environmental signals such as light. In accordance with the various developmental options of the plasmodial cell we found that many P. polycephalum genes are alternatively spliced. Using 30 donor and 30 acceptor sites we determined the splicing signatures of this species. Comparisons to various other organisms including Dictyostelium, the closest relative, revealed that roughly half of the transcribed genes have no detectable counterpart, thus potentially defining species specific adaptations. On the other hand, we found highly conserved proteins, which are maintained in the metazoan lineage, but absent in D. discoideum or plants. These genes arose possibly in the last common ancestor of Amoebozoa and Metazoa but were lost in D. discoideum.
  
  
  CONCLUSIONS
  This work provides an analysis of up to half of the protein coding genes of Physarum polycephalum. The definition of splice motifs together with the description of alternatively spliced genes will provide a valuable resource for the ongoing genome project.
authors.affiliation: Leibniz Institute for Age Research-Fritz Lipmann Institute, Beutenbergstr, 11, D-07745 Jena, Germany. gernot@fli-leibniz.de
authors.forename: Gernot
authors.initials: G
authors.lastname: Glöckner
authors.forename: Georg
authors.initials: G
authors.lastname: Golderer
authors.forename: Gabriele
authors.initials: G
authors.lastname: Werner-Felmayer
authors.forename: Sonja
authors.initials: S
authors.lastname: Meyer
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Marwan
mesh_terms: D017398:Alternative Splicing; D000818:Animals; D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling; D017125:Genes, Protozoan / Q000235:genetics; D006801:Humans; D010802:Phylogeny; D016839:Physarum polycephalum / Q000166:cytology / Q000235:genetics* / Q000254:growth & development; D015398:Signal Transduction / Q000235:genetics