Schaap, Pauline ORCID: 0000-0003-4500-2555, Barrantes, Israel, Minx, Pat, Sasaki, Narie, Anderson, Roger W., Beinard, Marianne, Biggar, Kyle K., Buehler, Nicolas E., Bundschuh, Ralf, Chen, Xiao, Fronick, Catrina, Fulton, Lucinda, Golderer, Georg, Jahn, Niels, Knoop, Volker, Landweber, Laura F., Maric, Chrystelle, Miller, Dennis, Noegel, Angelika A., Peace, Rob, Pierron, Gerard, Sasaki, Taeko, Schallenberg-Ruedinger, Mareike, Schleicher, Michael, Singh, Reema, Spaller, Thomas, Storey, Kenneth B., Suzuki, Takamasa, Tomlinson, Chad, Tyson, John J., Warren, Wesley C., Werner, Ernst R. ORCID: 0000-0003-1948-3391, Werner-Felmayer, Gabriele ORCID: 0000-0002-2340-8063, Wilson, Richard K. ORCID: 0000-0002-1992-1358, Winckler, Thomas, Gott, Jonatha M., Gloeckner, Gernot and Marwan, Wolfgang (2016). The Physarum polycephalum Genome Reveals Extensive Use of Prokaryotic Two-Component and Metazoan-Type Tyrosine Kinase Signaling. Genome Biol. Evol., 8 (1). S. 109 - 126. OXFORD: OXFORD UNIV PRESS. ISSN 1759-6653

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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.

Item Type: Journal Article
Creators:
CreatorsEmailORCIDORCID Put Code
Schaap, PaulineUNSPECIFIEDorcid.org/0000-0003-4500-2555UNSPECIFIED
Barrantes, IsraelUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Minx, PatUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Sasaki, NarieUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Anderson, Roger W.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Beinard, MarianneUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Biggar, Kyle K.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Buehler, Nicolas E.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Bundschuh, RalfUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Chen, XiaoUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Fronick, CatrinaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Fulton, LucindaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Golderer, GeorgUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Jahn, NielsUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Knoop, VolkerUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Landweber, Laura F.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Maric, ChrystelleUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Miller, DennisUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Noegel, Angelika A.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Peace, RobUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Pierron, GerardUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Sasaki, TaekoUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Schallenberg-Ruedinger, MareikeUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Schleicher, MichaelUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Singh, ReemaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Spaller, ThomasUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Storey, Kenneth B.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Suzuki, TakamasaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Tomlinson, ChadUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Tyson, John J.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Warren, Wesley C.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Werner, Ernst R.UNSPECIFIEDorcid.org/0000-0003-1948-3391UNSPECIFIED
Werner-Felmayer, GabrieleUNSPECIFIEDorcid.org/0000-0002-2340-8063UNSPECIFIED
Wilson, Richard K.UNSPECIFIEDorcid.org/0000-0002-1992-1358UNSPECIFIED
Winckler, ThomasUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Gott, Jonatha M.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Gloeckner, GernotUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Marwan, WolfgangUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
URN: urn:nbn:de:hbz:38-292744
DOI: 10.1093/gbe/evv237
Journal or Publication Title: Genome Biol. Evol.
Volume: 8
Number: 1
Page Range: S. 109 - 126
Date: 2016
Publisher: OXFORD UNIV PRESS
Place of Publication: OXFORD
ISSN: 1759-6653
Language: English
Faculty: Unspecified
Divisions: Unspecified
Subjects: no entry
Uncontrolled Keywords:
KeywordsLanguage
RNA EDITING FACTORS; PROTEIN-KINASE; DICTYOSTELIUM-DISCOIDEUM; SHIKIMATE PATHWAY; GENE-TRANSFER; PPR PROTEINS; ACTIN; CYCLE; SPORULATION; EVOLUTIONMultiple languages
Evolutionary Biology; Genetics & HeredityMultiple languages
Refereed: Yes
URI: http://kups.ub.uni-koeln.de/id/eprint/29274

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