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  The Physarum polycephalum Genome Reveals Extensive Use of Prokaryotic Two-Component and Metazoan-Type Tyrosine Kinase Signaling

Schaap, P., Barrantes Bustinza, I. W., Minx, P., Sasaki, N., Anderson, R. W., Bénard, M., et al. (2016). The Physarum polycephalum Genome Reveals Extensive Use of Prokaryotic Two-Component and Metazoan-Type Tyrosine Kinase Signaling. Genome Biology and Evolution, 8(1), 109-125. doi:10.1093/gbe/evv237.

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Item Permalink: http://hdl.handle.net/21.11116/0000-0001-23E8-2 Version Permalink: http://hdl.handle.net/21.11116/0000-0001-23E9-1
Genre: Journal Article

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 Creators:
Schaap, Pauline1, Author
Barrantes Bustinza, Israel W.2, 3, Author              
Minx, Pat4, Author
Sasaki, Narie5, Author
Anderson, Roger W.6, Author
Bénard, Marianne 7, Author
Biggar , Kyle K., Author
Buchler , Nicolas E. 8, Author
Bundschuh , Ralph9, Author
Chen, Xiao10, Author
Fronick, Catrina 4, Author
Fulton , Lucinda4, Author
Golderer, Georg11, Author
Jahn, Niels12, Author
Knoop, Volker13, Author
Landweber, Laura F. 10, Author
Maric , Chrystelle 14, Author
Miller, Dennis15, Author
Noegel , Angelika A. 16, Author
Peace, Rob 17, Author
Pierron, Gérard 14, AuthorSasaki , Taeko 5, AuthorSchallenberg-Rüdinger , Mareike 13, AuthorSchleicher, Michael 18, AuthorSingh, Reema 1, AuthorSpaller , Thomas 19, AuthorStorey , Kenneth B. 17, AuthorSuzuki , Takamasa 20, AuthorTomlinson, Chad 4, AuthorTyson, John J. 21, Author Warren , Wesley C.4, AuthorWerner , Ernst R. 11, AuthorWerner-Felmayer, Gabriele 11, AuthorWilson, Richard K. 4, AuthorWinckler , Thomas 19, AuthorM. Gott , Jonatha 22, AuthorGlöckner , Gernot 23, AuthorMarwan, Wolfgang2, Author more..
Affiliations:
1School of Life Sciences, University of Dundee, Dundee, United Kingdom, ou_persistent22              
2Otto-von-Guericke-Universität Magdeburg, External Organizations, ou_1738156              
3International Max Planck Research School (IMPRS), Max Planck Institute for Dynamics of Complex Technical Systems, Max Planck Society, ou_1738143              
4The Genome Institute, Washington University School of Medicine, St Louis, USA, ou_persistent22              
5Department of Biological Sciences, Graduate School of Science, Nagoya University, Furocho, Chikusaku, Nagoya, Aichi, Japan, ou_persistent22              
6Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, United Kingdom, ou_persistent22              
7UPMC Univ Paris 06, Institut de Biologie Paris-Seine (IBPS), Paris, France, ou_persistent22              
8Department of Biology and Center for Genomic and Computational Biology, Duke University, Durham Department of Physics, Duke University, Durham, ou_persistent22              
9 Department of Physics and Center for RNA Biology, The Ohio State University, Columbus Department of Chemistry & Biochemistry, The Ohio State University, Columbus Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, ou_persistent22              
10Department of Ecology & Evolutionary Biology, Princeton University, Princeton, ou_persistent22              
11Biological Chemistry, Biocenter, Innsbruck Medical University, Innsbruck, Austria, ou_persistent22              
12Genome Analysis, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany, ou_persistent22              
13IZMB - Institut für Zelluläre und Molekulare Botanik, Universität Bonn, Bonn, Germany, ou_persistent22              
14Institut Jacques Monod, CNRS UMR7592, Université Paris Diderot Paris7, Paris, France, ou_persistent22              
15The University of Texas at Dallas, Biological Sciences, Richardson, USA, ou_persistent22              
16Institute for Biochemistry I, Medical Faculty, University of Cologne, Cologne, Germany, ou_persistent22              
17Carleton University, Ottawa, Ontario, Canada, ou_persistent22              
18Institute for Anatomy III / Cell Biology, BioMedCenter, Ludwig-Maximilians-Universität, , Planegg-Martinsried, Germany, ou_persistent22              
19Institut für Pharmazie, Friedrich-Schiller-Universität Jena, Jena, Germany, ou_persistent22              
20Department of Biological Sciences, Graduate School of Science and JST ERATO Higashiyama Live-holonics Project, Nagoya University, Furocho, Chikusaku, Nagoya, Aichi, Japan., Nagoya, Aichi, Japan, ou_persistent22              
21Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, USA, ou_persistent22              
22Center for RNA Molecular Biology, Case Western Reserve University, School of Medicine, Cleveland, USA, ou_persistent22              
23Institute for Biochemistry I, Medical Faculty, University of Cologne, Cologne, Germany Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany, ou_persistent22              

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 Abstract: 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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Language(s): eng - English
 Dates: 2016
 Publication Status: Published in print
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Method: Peer
 Identifiers: DOI: 10.1093/gbe/evv237
 Degree: -

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Title: Genome Biology and Evolution
  Other : GBE
  Abbreviation : Genome Biol Evol
Source Genre: Journal
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Publ. Info: Oxford : Oxford Univ. Press
Pages: - Volume / Issue: 8 (1) Sequence Number: - Start / End Page: 109 - 125 Identifier: Other: 1759-6653
CoNE: https://pure.mpg.de/cone/journals/resource/1759-6653