Andrew Thompson and Braasch Lab Unpack Genome Sequence from Rio Pearlfish

Rio pearlfish has long been of particular interest to Andrew (Drew) Thompson, a postdoctoral research associate in Ingo Braasch's Fish Evo Devo Geno Lab. “We can learn a lot from this species,” he said. “If we can understand how they control their growth and development, maybe we can understand it better in humans, too. There is a lot of potential to inform studies of human health and disease.”

Braasch's team have sequenced the first complete genome of the fish. With that genome, researchers can better understand the biology and evolution of the species’ survival skills. The team also captured the full 3-D structure of the genome, which helps illuminate how and when genes turn on and interact with each other. All of this new information strengthens the Rio pearlfish’s potential as a model organism that can further understanding of human health.

Ingo said, "Drew’s meticulous studies of numerous killifish species over several years revealed that the Rio pearlfish is an ideal research organism to study fundamental questions about the genetic basis of animal development and evolution. They are some of the most fascinating ‘superheroes’ of the fish world.”

Rio pearlfish are a type of fish known as annual killifish that live in puddles that form in and around Rio de Janeiro, Brazil, during the region’s two rainy seasons. Those are followed by dry seasons that run from February to March and July into August. During these dry spells, the pools dry up and the grown pearlfish populations are wiped out. Their eggs, however, survive by essentially going dormant, entering what’s known as diapause.

Drew said, “The embryos stop developing and slow their metabolism so they can wait out the dry seasons and hatch at the proper time. It’s really rare for a vertebrate to stop its development and do this suspended animation.”

Examining the genetics of this adaptation could thus provide clues about what’s happening at a molecular level in human developmental disorders. On the flip side, a better understanding of the natural “hypersleep” of diapause could also help humans working to use suspended animation to make surgeries safer and extended space travel possible.

“We can use these fish for a lot of really cool studies in evolution, aging, suspended animation and hatching,” Drew said. “Every vertebrate hatches, even humans.” Approximately a week after eggs are fertilized, embryos release enzymes to shed their egg envelopes and continue growing. 

Thanks to Drew and undergraduate researchers Myles Davoll and Harrison Wojtas, science now know not only the genes involved in making the enzymes, but also where the gland that makes those enzymes is located. Fun fact: It’s in the pearlfish’s mouth.

“It was really great working with these two really talented undergrads,” Drew said. “Myles and Harrison were the ones who dug into analyzing the hatching enzymes and found one of the coolest things we discovered about these fish."

Davoll was a visiting student from Clemson University who is now a graduate student at the University of Virginia. Wojtas was a Larry D. Fowler Fellow who is now an educator at the Sitka Sound Science Center in Sitka, Alaska.

Although there are important differences in how humans and killifish hatch, researchers who want to learn more about early human development can now consider using Rio pearlfish as a model. And, unlike mammalian model organisms such as mice, the killifish hatch outside of the mother for all to see.