Sponge Genomes: Simply Complex

You might not think much of sponges. Maybe you feel that they’re only good for rubbing your back and cleaning your kitchen sink. While you’re absolutely right that sponges have to be admired for their absorbing qualities, they have much more to offer this world. Like on the front of early animal evolution: new research by a Croatian team of scientists shows that these simple creatures harbour a genomic complexity that matches our own!

Sponges really are pretty cool animals. As an example, Henry van Peters Wilson discovered the regenerative abilities of sponges in 1907 by sieving a living sponge, thereby fragmenting its cells. Afterwards he saw that the remaining clumps of cells found each other again to form what he called ‘plasmodial masses’. After a while, complete sponges emerged again from these ‘masses’!

This remarkable regenerative flexibility might partly reflect the transition that their ancestors underwent from a colonial to a multicellular species (scientists believe sponges evolved from colonies of protozoans much like Monosiga brevicollis). Sponges can lay claim to being the first animals on this planet, and the common ancestor of all animals might very well have been a very sponge-like critter.

Spongia officinalis, or "kitchen sponge". It is dark grey because it is alive, unlike the dried out yellow one in your bathtub. Source.

Sponges are morphologically not very complex. They depend on the flow of water to obtain food and oxygen and remove their waste products. Their porous body structure and skeleton are built to optimize this flow of water, making it flow through all interconnected chambers. Sponges have a number of different cell types, with some that can generate the water flow with their beating flagella, some that can contract and transmit signals like muscle cells and others that maintain and repair the sponge ‘skeleton’.

Such a simple animal must have a pretty simple genome right? Not exactly. Matija Harcet and colleagues sequenced a large set of expressed genes from two different sponges and compared them to their homologs from sea anemone , sea squirt , nematode , fruit fly, sea urchin and human. As you can see in the phylogenetic tree below, the sponges (porifera) occupy a basal position on the tree of metazoans. Consider the surprise when most sponge gene transcripts mapped back to the human and sea anemone proteomes, whereas nematodes and fruit flies ranked the lowest on the list!

Phylogenetic relationships between sponges (porifera) and other animals. We humans are hiding within "Chordata", sea squirts within "Tunicata" and sea urchins in "Echinodermata".

Moreover, the sponge transcripts not only matched the most genes in sea anemones and humans, the protein sequences were also much more similar to human genes than those of other species. You can see this for yourself in the beautiful figure below. Every dot is a transcript that is placed closest to the species it is most similar to. The sponge transcripts most often fall in the human or sea anemone (N. vectensis) quadrants.

A possible explanation for this observation could be that genes have been evolving slowly in both sponges and humans, whereas the proteins of nematodes and drosophila have been evolving in overdrive. Since these species have much shorter generation times and larger population sizes, they can acquire mutations at a much higher rate, speeding up the sequence evolution of their genes.

Each dot is an EST plotted at the appropriate relative sequence distance from the other species.

The team also compared the sponge gene repertoire to that of our closest unicellular nephew: the Monosiga brevicollis that was mentioned before. They found more than a thousand genes which were unique to sponges, of which most are predicted to be involved in signalling pathways and cel adhesion processes. This would mean that most gene expansions and genomic innovations that are found in animals today, were already present in the Urmetazoan ancestor of all animals.

Whatever happened in that great-great grandmother of animals, she spawned the whole breadth of animals of the Cambrian explosion and those alive today. Sometimes, simple appearances hold complex and fascinating stories. Not bad, for a ‘simple’ sponge!

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