Comparative genomics of the social amoebae Dictyostelium discoideum and Dictyostelium purpureum

Richard Sucgang, Alan Kuo, Xiangjun Tian, William Salerno, Anup Parikh, Christa L. Feasley, Eileen Dalin, Hank Tu, Eryong Huang, Kerrie Barry, Erika Lindquist, Harris Shapiro, David Bruce, Jeremy Schmutz, Asaf Salamov, Petra Fey, Pascale Gaudet, Christophe Anjard, M. Madan Babu, Siddhartha BasuYulia Bushmanova, Hanke van der Wel, Mariko Katoh-Kurasawa, Christopher Dinh, Pedro M. Coutinho, Tamao Saito, Marek Elias, Pauline Schaap, Robert R. Kay, Bernard Henrissat, Ludwig Eichinger, Francisco Rivero, Nicholas H. Putnam, Christopher M. West, William F. Loomis, Rex L. Chisholm, Gad Shaulsky, Joan E. Strassmann, David C. Queller, Adam Kuspa, Igor V. Grigoriev

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    107 Citations (Scopus)

    Abstract

    Background: The social amoebae (Dictyostelia) are a diverse group of Amoebozoa that achieve multicellularity by aggregation and undergo morphogenesis into fruiting bodies with terminally differentiated spores and stalk cells. There are four groups of dictyostelids, with the most derived being a group that contains the model species Dictyostelium discoideum.

    Results: We have produced a draft genome sequence of another group dictyostelid, Dictyostelium purpureum, and compare it to the D. discoideum genome. The assembly (8.41 x coverage) comprises 799 scaffolds totaling 33.0 Mb, comparable to the D. discoideum genome size. Sequence comparisons suggest that these two dictyostelids shared a common ancestor approximately 400 million years ago. In spite of this divergence, most orthologs reside in small clusters of conserved synteny. Comparative analyses revealed a core set of orthologous genes that illuminate dictyostelid physiology, as well as differences in gene family content. Interesting patterns of gene conservation and divergence are also evident, suggesting function differences; some protein families, such as the histidine kinases, have undergone little functional change, whereas others, such as the polyketide synthases, have undergone extensive diversification. The abundant amino acid homopolymers encoded in both genomes are generally not found in homologous positions within proteins, so they are unlikely to derive from ancestral DNA triplet repeats. Genes involved in the social stage evolved more rapidly than others, consistent with either relaxed selection or accelerated evolution due to social conflict.

    Conclusions: The findings from this new genome sequence and comparative analysis shed light on the biology and evolution of the Dictyostelia.

    Original languageEnglish
    Article numberR20
    Pages (from-to)-
    Number of pages23
    JournalGenome Biology
    Volume12
    Issue number2
    DOIs
    Publication statusPublished - Feb 2011

    Keywords

    • Differentiation inducing factor
    • Cellular slime mold
    • Multiple sequence alignment
    • Adenylyl cyclase
    • Terminal differentiation
    • Polyketides synthase
    • Natural products
    • Cheater mutants
    • Protein kinases
    • Noncoding RNAS

    Cite this

    Sucgang, R., Kuo, A., Tian, X., Salerno, W., Parikh, A., Feasley, C. L., Dalin, E., Tu, H., Huang, E., Barry, K., Lindquist, E., Shapiro, H., Bruce, D., Schmutz, J., Salamov, A., Fey, P., Gaudet, P., Anjard, C., Babu, M. M., ... Grigoriev, I. V. (2011). Comparative genomics of the social amoebae Dictyostelium discoideum and Dictyostelium purpureum. Genome Biology, 12(2), -. [R20]. https://doi.org/10.1186/gb-2011-12-2-r20