An international team of researchers from 40 institutions across 12 countries - including the Broad Institute at Harvard/MIT, the University of the Western Cape (UWC) and Rhodes University - has decoded the genome of the world's most famous "living fossil": the African coelacanth.
Rediscovered in 1938 after having thought to have been extinct for at least 70 million years, these sea-cave dwelling, five-foot long fish with limb-like fins closely resemble the fossilised skeletons of their ancestors from 300 million years ago. The decoded 3 billion-letter genome confirms long-held suspicions that genes in the coelacanth are evolving more slowly than in other organisms - and also sheds light on the evolution of land-living vertebrates (tetrapods) from fish ancestors.
“We found that the genes overall are evolving significantly slower than in every other fish and land vertebrate that we looked at,” says Jessica Alföldi, a research scientist at the Broad Institute and co-first author of a paper on the coelacanth genome, which appears in Nature this week. “This is the first time that we’ve had a big enough gene set to really see that.”
Researchers hypothesise that this slow rate of change may be because coelacanths simply have not needed to change: they live primarily off of the Eastern African coast (a second coelacanth species lives off the coast of Indonesia), at ocean depths where relatively little has changed over the millennia. "It's not a living fossil; it’s a living organism,” says Alföldi. “It doesn’t live in a time bubble; it lives in our world, which is why it’s so fascinating to find out that its genes are evolving more slowly than ours.”
The coelacanth genome has also allowed scientists to test other long-debated questions. For example, coelacanths possess “lobed” fins, which resemble the limbs of four-legged land animals (known as tetrapods). Another odd-looking group of fish, known as lungfish, also possesses lobed fins. It is likely that one of the ancestral lobed-finned fish species gave rise to the first four-legged amphibious creatures to climb out of the water and up onto land - but until now, researchers could not determine which of the two is the more likely candidate.
In addition to sequencing the full genome from the coelacanth, the researchers also looked at RNA content from coelacanth (both the African and Indonesian species) and from the lungfish. This information allowed them to compare genes in use in the brain, kidneys, liver, spleen and gut of lungfish with gene sets from coelacanth and 20 other vertebrate species. Their results suggested that tetrapods are more closely related to lungfish than to the coelacanth.
However, the coelacanth is still a critical organism to study in order to understand what is often called the water-to-land transition. Lungfish may be more closely related to land animals, but at 100 billion letters in length, the lungfish genome is simply too unwieldy for scientists to sequence, assemble, and analyse. The coelacanth’s more modest-sized genome (comparable in length to our own) is yielding valuable clues about the genetic changes that may have allowed tetrapods to flourish on land.
South African lead researcher Professor Alan Christoffels started working on a coelacanth project 10 years ago in Singapore, when he was part of a team that analysed the developmental genes (HOX genes) of the coelacanth. At that time there was no completely sequenced genome sequence. About a year ago, Christoffels was invited to participate in the genomic analysis of the Coelacanth genome, together with his team from UWC’s South African Bioinformatics Institute (SANBI-UWC). The team included three postdocs – namely Drs Picone, Hesse and Panji – as well as software programmer Peter van Heusden and SANBI staff members Dr Junaid Gamieldien and Mario Jonas.
“Scientists have reported extensively on the coelacanth as a model for understanding vertebrate adaptation to land,” notes Christoffels. “Only with the entire genome sequence could researchers start identifying functional units in the coelacanth DNA that are involved in fin-to-limb transition.”
By looking at what genes were lost when vertebrates came on land as well as what regulatory elements – parts of the genome that govern where, when, and to what degree genes are active – were gained, the international assemblage of researchers made several unusual discoveries:
Sense of smell. The team found that many regulatory changes influenced genes involved in smell perception and detecting airborne odours. They hypothesise that as creatures moved from sea to land, they needed new means of detecting chemicals in the environment around them.
Immunity. The researchers found a significant number of immune-related regulatory changes when they compared the coelacanth genome to the genomes of animals on land. They hypothesised that these changes may be part of a response to new pathogens encountered on land.
Evolutionary development. Researchers found several key genetic regions that may have been “evolutionarily recruited” to form tetrapod innovations such as limbs, fingers and toes, and the mammalian placenta. One of these regions, known as HoxD, harbours a particular sequence that is shared across coelacanths and tetrapods. It is likely that this sequence from the coelacanth was co-opted by tetrapods to help form hands and feet.
Urea cycle. Fish get rid of nitrogen by excreting ammonia into the water, but humans and other land animals quickly convert ammonia into less toxic urea using the urea cycle. Researchers found that the most important gene involved in this cycle has been modified in tetrapods.
“Each of the international teams focused on one aspect of the evolution of this species. We identified what is called "gene expansions" in this ancient organism and found that some of these multiple copies of the same gene are peculiar to coelacanth. This phenomenon usually indicates new adaptations in the context of an organism’s functions. More specifically we identified a class of olfactory genes whose function fits a model for vertebrate adaptation,” says Christoffels. SANBI will be publishing the results of its analysis of olfactory genes in coelacanth shortly.
Sequencing the full coelacanth genome was uniquely challenging. Coelacanths are endangered animals, meaning that samples available for research are almost nonexistent. This meant that each sample obtained was precious: researchers would have one shot at sequencing the collected genetic material. But the difficulties in obtaining a sample and the challenges of sequencing it also knit the community together.
Many funding agencies around the world provided support for this work, including the South African Institute for Aquatic Biodiversity (SAIAB) African Coelacanth Ecosystem Programme (ACEP) funded by the South African National Department of Science and Technology, which supported the collection of samples from coelacanths found off Sodwana Bay on the East coast of South Africa, Rhodes University, and the National Human Genome Research Institute, which supported the Broad Institute’s contributions, including genome sequencing.