Sponges are likely to be the oldest of the surviving animal lineages. In contrast to the eumetazoans (complex animals such as corals, insects and vertebrates), sponges have no nerves, muscles or gut, but their regenerating abilities are truly spectacular. Over a decade ago, analysis of the first sequenced sponge genome (of the demosponge Amphimedon) demonstrated that development of the simple sponge body plan is governed by a limited number of regulatory genes, suggesting a gradual assembly of the complex eumetazoan developmental toolkit.
However, sponges are a diverse phylum, composed of four distinct lineages: demosponges, hexactinellids, calcisponges and homoscleromorphs. We have sequenced genomes and transcriptomes of several calcisponges, including calcaroneans (Sycon and Leucosolenia) and calcineans (Clathrina and Pericharax), and a demosponge distantly related to Amphimedon (Halisarca). For some, we have also generated transcriptome datasets representing embryonic and postembryonic development and regeneration.
We have uncovered unexpected complexity and diversity of developmental toolkits among sponges, with calcisponge developmental regulatory gene families generally more complex than those in demosponges. Significant gene losses must have occurred independently in the calcisponge and demosponge lineages, followed by gene family expansions occurring independently in the calcaronean and calcinean lineages, and leading to spectacular developmental toolkit diversity among sponge species.
Gene expression analysis suggests deep conservation of body plan patterning and regeneration mechanisms between sponges and the eumetazoans. For example, the Wnt and TGF-beta pathways appear to be involved in specification of the larval and adult body plans, as well as regeneration of sponges. Genes involved in wound healing of calcisponges, and activated within minutes of injury, include Fos-Jun and Grainyhead transcription factors, known to regulate wound healing in Drosophila and vertebrates.
Overall, while sponges are clearly not “living fossils”, they provide a wonderful window into the evolutionary history and evolvability of animal genomes.