Ghosts in sponge genomes and finding the bullet from the smoking gun
A team of scientists from the University of St Andrews Scottish Oceans Institute and the Sars Centre at the University of Bergen, have revealed that the last common ancestor of all animals was more complex than previously thought.
In a new study, published today in scientific journal Nature, researchers report the analysis of new sponge genome sequences that reveal the presence of genes previously unknown from so early in animal evolution.
Previous research from the University of St Andrews suggested that important genes controlling animal development had been lost from some sponges, leaving ghost loci – otherwise known as ‘neighbourhoods’. Similar to the genomic neighbourhoods in humans and other animals, these are ghost-like because the developmental gene has died and disappeared, leaving behind a ghostly outline of its surroundings. This would mean that the earliest animal, living over 600 million years ago, was genetically more complex than previously appreciated.
Sponges are one of the earliest branches of the animal tree of life and are key organisms in understanding the nature of the last common ancestor of all animals. With newly sequenced sponge genomes, the bullet from the ‘ghost loci’ smoking gun has now been found. This new research reports sponges with the “lost” genes now present in the neighbourhoods that are ghost loci in the previously sequenced sponges.
Dr David Ferrier, from the University of St Andrews Scottish Oceans Institute, and the team studied key genes known as Hox and ParaHox, which are renowned for building the bodies of nearly all modern day animals, including the development of our nervous systems and guts – they can also be disrupted in diseases such as cancer and diabetes.
By analysing the homeobox genes of two sponge species that make calcified spicules –or spines found all over the body wall - the researchers found a clear ParaHox gene called Cdx. In one of the sponges, the Cdx gene is expressed in sponge cells that are thought to be the evolutionary equivalent to cells found in our guts. This is also where the human Cdx is expressed, being linked to some colon cancers when it goes wrong.
Dr David Ferrier, lead researcher at the University of St Andrews, explains:
“The reason that this is so exciting is that our previous work, identifying ghost loci, still remained rather controversial to some people. They worried that we might have been misled by some form of rare genome rearrangement or mutation. Finding a bona fide Cdx gene really is like finding the bullet from the smoking gun and can finally lay a lot of the controversy to rest.”
Dr Maja Adamska, lead researcher of the University of Bergen group, adds:
“The genomes of these calcisponges that we’ve sequenced reveal that the developmental toolkits of sponges vary dramatically. It is clear that we need to study a much wider range of species than are commonly used, in order to understand the complexity of the very first animal and how the huge diversity that we see around us today evolved from this initial ancestor that lived over 600 million years ago.”