The physarum polycephalum genome reveals extensive use of prokaryotic two-component and metazoan-type tyrosine kinase signaling

Physarum polycephalum is a well-studied microbial eukaryote with unique experimental attributes relative to other experimental model organisms. It has a sophisticated life cycle with several distinct stages including amoebal, flagellated, and plasmodial cells. It is unusual in switching between open and closed mitosis according to specific life-cycle stages. Here we present the analysis of the genome of this enigmatic and important model organism and compare it with closely related species. The genome is littered with simple and complex repeats and the coding regions are frequently interrupted by introns with a mean size of 100 bases. Complemented with extensive transcriptome data, we define approximately 31,000 gene loci, providing unexpected insights into early eukaryote evolution.Wedescribe extensiveuse of histidine kinase-based two-component systems andtyrosine kinase signaling, the presence of bacterial and plant type photoreceptors (phytochromes, cryptochrome, and phototropin) and of plant-type pentatricopeptide repeat proteins, aswell asmetabolic pathways, and a cell cycle control system typically found in more complex eukaryotes. Our analysis characterizes P. polycephalumas a prototypical eukaryote with features attributed to the last common ancestor of Amorphea, that is, theAmoebozoa andOpisthokonts. Specifically, the presence of tyrosine kinases in Acanthamoeba and Physarum as representatives of twodistantly related subdivisions ofAmoebozoa argues against the lateremergence of tyrosine kinase signaling in the opisthokont lineage and also against the acquisition by horizontal gene transfer.