Phylogeny-wide analysis of social amoeba genomes highlights ancient origins for complex intercellular communication

Andrew J. Heidel, Hajara M. Lawal, Marius Felder, Christina Schilde, Nicholas R. Helps, Budi Tunggal, Francisco Rivero, Uwe John, Michael Schleicher, Ludwig Eichinger, Matthias Platzer, Angelika A. Noegel, Pauline Schaap (Lead / Corresponding author), Gernot Gloeckner (Lead / Corresponding author)

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    91 Citations (Scopus)

    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.

    Original languageEnglish
    Pages (from-to)1882-1891
    Number of pages10
    JournalGenome Research
    Volume21
    Issue number11
    Early online date14 Jul 2011
    DOIs
    Publication statusPublished - Nov 2011

    Keywords

    • III Polyketide synthase
    • Dictyostelium discoideum (Dd)
    • Terminal differentiation
    • Transposable elements
    • Entamoeba histolytica
    • ABC transporters
    • RNA genes
    • Evolution
    • Sequence
    • CAMP

    Cite this

    Heidel, A. J., Lawal, H. M., Felder, M., Schilde, C., Helps, N. R., Tunggal, B., Rivero, F., John, U., Schleicher, M., Eichinger, L., Platzer, M., Noegel, A. A., Schaap, P., & Gloeckner, G. (2011). Phylogeny-wide analysis of social amoeba genomes highlights ancient origins for complex intercellular communication. Genome Research, 21(11), 1882-1891. https://doi.org/10.1101/gr.121137.111