Journal
GENOME BIOLOGY AND EVOLUTION
Volume 8, Issue 1, Pages 109-125Publisher
OXFORD UNIV PRESS
DOI: 10.1093/gbe/evv237
Keywords
Amoebozoa; tyrosine kinase receptor; two-component system; signaling; phytochrome
Categories
Funding
- National Institutes of Health (NIH) [HG003079, GM54663]
- Genome Institute at Washington University School of Medicine
- Wellcome Trust [100293/Z/12/Z]
- BBSRC [BB/K000799/1]
- International Max Planck Research School, Magdeburg
- German Federal Ministry of Education and Research (BMBF) via FORSYS program [FKZ 0313922]
- Austrian Science Fund (EWE) [P22406]
- National Science Foundation (NSF) [MCB-1243687]
- Biotechnology and Biological Sciences Research Council [BB/K000799/1] Funding Source: researchfish
- NATIONAL HUMAN GENOME RESEARCH INSTITUTE [U54HG003079] Funding Source: NIH RePORTER
- NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES [R01GM054663, R55GM054663] Funding Source: NIH RePORTER
- Direct For Biological Sciences [1243687] Funding Source: National Science Foundation
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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. We describe extensive use of histidine kinase-based two-component systems and tyrosine kinase signaling, the presence of bacterial and plant type photoreceptors (phytochromes, cryptochrome, and phototropin) and of plant-type pentatricopeptide repeat proteins, as well as metabolic pathways, and a cell cycle control system typically found in more complex eukaryotes. Our analysis characterizes P. polycephalum as a prototypical eukaryote with features attributed to the last common ancestor of Amorphea, that is, the Amoebozoa and Opisthokonts. Specifically, the presence of tyrosine kinases in Acanthamoeba and Physarum as representatives of two distantly related subdivisions of Amoebozoa argues against the later emergence of tyrosine kinase signaling in the opisthokont lineage and also against the acquisition by horizontal gene transfer.
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