The first complete sequence of a seahorse genome finds the genetic roots of the tropical creature’s unusual shape and characteristics.
The findings could also explain many features common to the entire animal kingdom, including hind-limb and mineralized-teeth development in humans. “Fish and humans have a similar set of genes,” says Byrappa Venkatesh at the A*STAR Institute of Molecular and Cell Biology, who led the study. “Investigating the seahorse genome can help us to understand human biology and human disease better.”
While classified as fish, seahorses more closely resemble the ‘horse caterpillar’ alluded to in their Latin name, Hippocampus. Instead of scales, seahorses are covered in rugged, bony armor. They also lack the tail fin and pelvic fins needed for propulsion and steering, preferring to trot upright, anchoring on to grasses and corals with their coiled tails.
Their tiny, toothless mouths suck food up elongated snouts; and seahorse fathers nurse their young in a brood pouch.
Venkatesh and his colleagues wanted to find the parts of the seahorse genome that give rise to these peculiar features.
They collected samples from a species endemic to the Asia-Pacific region — the tiger tail seahorse — and conducted whole genome shotgun sequencing, which involves sequencing fragments of DNA and reassembling the strands in a computer. They then compared the seahorse genome to those of other fish, including the zebrafish, stickleback and Nile tilapia.
The researchers found that much of the seahorse’s strange anatomy could be explained by the loss of specific genes. Seahorses lack tbx4, an important gene for pelvic fin formation and the development of hind legs in land animals. They are also missing crucial genes that encode the enamel proteins in teeth, and have a sparse repertoire of receptors required for smell. “This suggests that seahorses don’t use the sense of smell as extensively as other fishes for avoiding predators or finding food and mates,” says Venkatesh.
Seahorses have also acquired several genetic abilities. In a more detailed analysis of the male brood pouch, the researchers counted significantly higher expression levels of a cluster of novel pregnancy-associated genes called patristacins.
Most surprising for Venkatesh was the genome’s speed of evolution from a common fish ancestor. “Seahorses are very sluggish animals, but if you look inside their DNA, it has been changing very rapidly compared to other fish.”
The team hope to extend their genomic analysis to study the fish’s population size and change over time. Most seahorse species on the IUCN Red List of Threatened Species are categorized as vulnerable, with decreasing or unknown population trends. “Genome sequencing will help in coming up with measures to conserve their stock.”
The A*STAR-affiliated researchers contributing to this research are from the Institute of Molecular and Cell Biology.