title: Phylogeny-wide analysis of social amoeba genomes highlights ancient origins for complex intercellular communication.
abstract: Dictyostelium discoideum (DD), an extensively studied model organism for cell and developmental biology, belongs to the most derived group 4 of social amoebas, a clade of altruistic multicellular organisms. To understand genome evolution over long time periods and the genetic basis of social evolution, we sequenced the genomes of Dictyostelium fasciculatum (DF) and Polysphondylium pallidum (PP), which represent the early diverging groups 1 and 2, respectively. In contrast to DD, PP and DF have conventional telomere organization and strongly reduced numbers of transposable elements. The number of protein-coding genes is similar between species, but only half of them comprise an identifiable set of orthologous genes. In general, genes involved in primary metabolism, cytoskeletal functions and signal transduction are conserved, while genes involved in secondary metabolism, export, and signal perception underwent large differential gene family expansions. This most likely signifies involvement of the conserved set in core cell and developmental mechanisms, and of the diverged set in niche- and species-specific adaptations for defense and food, mate, and kin selection. Phylogenetic dating using a concatenated data set and extensive loss of synteny indicate that DF, PP, and DD split from their last common ancestor at least 0.6 billion years ago.
authors.affiliation: Leibniz Institute for Age Research-Fritz Lipmann Institute, D-07745 Jena, Germany.
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Heidel
authors.forename: Hajara M
authors.initials: HM
authors.lastname: Lawal
authors.forename: Marius
authors.initials: M
authors.lastname: Felder
authors.forename: Christina
authors.initials: C
authors.lastname: Schilde
authors.forename: Nicholas R
authors.initials: NR
authors.lastname: Helps
authors.forename: Budi
authors.initials: B
authors.lastname: Tunggal
authors.forename: Francisco
authors.initials: F
authors.lastname: Rivero
authors.forename: Uwe
authors.initials: U
authors.lastname: John
authors.forename: Michael
authors.initials: M
authors.lastname: Schleicher
authors.forename: Ludwig
authors.initials: L
authors.lastname: Eichinger
authors.forename: Matthias
authors.initials: M
authors.lastname: Platzer
authors.forename: Angelika A
authors.initials: AA
authors.lastname: Noegel
authors.forename: Pauline
authors.initials: P
authors.lastname: Schaap
authors.forename: Gernot
authors.initials: G
authors.lastname: Glöckner
mesh_terms: D000595:Amino Acid Sequence / Q000235:genetics; D001482:Base Composition; D001692:Biological Transport; D002448:Cell Adhesion / Q000235:genetics; D002450:Cell Communication / Q000235:genetics; D002465:Cell Movement / Q000235:genetics; D002503:Centromere / Q000235:genetics / Q000378:metabolism; D003599:Cytoskeleton / Q000235:genetics; D004023:Dictyostelium / Q000235:genetics* / Q000378:metabolism; D019143:Evolution, Molecular; D018503:Genome, Protozoan; D008969:Molecular Sequence Data; D015394:Molecular Structure; D009712:Nucleotides, Cyclic / Q000378:metabolism; D016366:Open Reading Frames; D010802:Phylogeny; D054730:Protein Interaction Domains and Motifs; D015398:Signal Transduction; D026801:Synteny; D016615:Telomere / Q000235:genetics / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D009712:Nucleotides, Cyclic