What Makes A Fish Tick? Sequencing The Genome Of The Ocean Sunfish
By Bio-IT World Staff
September 16, 2016 | It’s fairly easy to be dwarfed by the ocean sunfish (Mola mola). Weighing on average 2.3 tons and measuring at length of 2.7m, this bony fish is one of the most unusual creatures in the ocean. What has researchers fascinated by the mammoth of a fish, however, is the staggering rate at which it grows. While other fish grow at a rate of about .02-.5 kilograms a day, the ocean sunfish grows at the astonishingly fast rate of 1 kilogram a day.
Researchers have been trying to solve the mystery of why the sunfish grows at such an alarming rate for years. The puzzle was of particular intrigue to Nobel Laureate Sydney Brenner, who, with a team of researchers, has been able to sequence the sunfish’s genome for the first time ever. The sequencing was conducted by researchers at A*STAR, Singapore, and China National Genebank, and the results were published in GigaScience (DOI: 10.1186/s13742-016-0144-3)
Brenner and his colleagues are no amateurs when it comes to sequencing the genomes of intriguing fish, having sequenced the genome of the pufferfish in 2002. The pufferfish and ocean sunfish belong to the same order, and so the decision to sequence the sunfish’s genome seemed to be an easy on to make. Brenner believes the sunfish to be the end of an evolutionary line.
A large problem was in finding a sample of the desired fish. “I tried for many years to obtain a sample but failed,” Brenner told Scott Edmunds, editor at GigaScience, for a blog post. It wasn’t until he relayed his interest while visiting the Marine sciences laboratory in Florida that things began to fall into place. Brenner remembers: “[a colleague] telephoned me one day to tell me that a mola mola had swum up the intercoastal canal and had been found by the private aquarium close to the Marine Laboratory. It would be exhibited there and when it died he would arrange for me get some blood.”
The sample of ocean sunfish blood was delivered to Brenner shortly after the death of the fish. Returning to Singapore with frozen blood sample tucked away in his hand luggage, Brenner began the process of genome sequencing. The process from Brenner’s acquiring the sample to the sunfish’s genome being sequenced would take 20 years.
The initial stages involved hypothesizing what factors resulted in the unique fish’s growth rate. One hypothesis the researchers considered was that the lack of HOX genes, a group of related genes that control the body plan of an animal, resulted in the enormous size of the sunfish. However, initial tests revealed that the sunfish’s HOX was in complete gene clusters. What they discovered to be the source of exponential growth was, according Associate Director of China National Genebank Guojie Zhang, “several genes involved in growth hormone signalling evolve very fast in the sunfish when compared to other bony fishes.”
Another uncommon trait of the sunfish is its skeletal makeup. While most bony fishes have skeletons made of bone (obviously), the sunfish’s skeleton is composed primarily of cartilage. “We found changes in genes encoding for collagen and cartilage formation. This may contribute to the development of predominantly cartilaginous skeleton in this gigantic fish,” says Byrappa Venkatesh, who initiated and led the project at the Institute of Molecular and Cell Biology in Singapore. “Vertebrates exhibit a wide diversity in their morphology, physiology and behavior. Understanding the genetic basis of this diversity is a major goal of evolutionary biology.”
There is still work to be done when it comes to unspooling the mysteries of the ocean sunfish. Venkatesh believes the key to solving these mysteries comes from sequencing other species closely related to the sunfish, such as the porcupine fish, box fish, and triggerfish. Perhaps these investigations will serve as a roadmap for researchers who have only begun to navigate their way through the mysterious genome of the ocean sunfish.