Comparative genomics of the social amoebae Dictyostelium discoideum and Dictyostelium purpureum

Abstract

BackgroundThe 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.ResultsWe have produced a draft genome sequence of another group dictyostelid, Dictyostelium purpureum, and compare it to the D. discoideum genome. The assembly (8.41 × 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.ConclusionsThe findings from this new genome sequence and comparative analysis shed light on the biology and evolution of the Dictyostelia.

Evolution of cooperation and control of cheating in a social microbe

“…In this analysis, the more social genes had a lower probability of having homologs, an elevated rate of amino acid change, and a lower conservation score, supporting our hypothesis (92). The result could also be attributable to weaker purifying selection on social genes, however, and a better analysis would be between more closely related species.…”

“…Our test of this hypothesis used the newly sequenced species D. purpureum and compared it with D. discoideum (92). Unfortunately, this is not an ideal pair of species because their proteins are as diverged as those of humans and fish.…”

Dictyostelium discoideum has a highly Q/N-rich proteome and shows an unusual resilience to protein aggregation

“…The first analysis of poly-amino acid stretches in D. discoideum showed that such sequences occur only in specific protein families (62). More recent work by Sucgang et al suggested that poly-amino acid repeats are microsatellites (29). Moreover, these authors provided data that contradict the notion that the N/Q-rich sequences are functional.…”

“…Apart from D. discoideum, D. purpureum is the only Dictyostelid whose genome has been sequenced and fully annotated (29). We found ∼900 candidate proteins in the proteome of D. purpureum (Dataset S1).…”

“…Previous studies have speculated about the functional significance of prion-like proteins in D. discoideum (29,62,63). The first analysis of poly-amino acid stretches in D. discoideum showed that such sequences occur only in specific protein families (62).…”