The project unveiled the 30,773 genes in the fish and localized them along chromosomes. It also pointed to genes that adapted or disappeared as the fish acclimated to higher oxygen concentrations beginning about 77 million years ago as the water cooled. Today’s Antarctic seawater temperature hovers just below the freezing point of fresh water.
Among genes that disappeared amid the months of night and months of sunlight in the polar region were those tied to circadian rhythms.
“We will now be able to mine this genome to learn how the fish evolved these seemingly pathogenic traits to their benefit,” said John Postlethwait, professor emeritus in the Department of Biology and member of the UO’s Institute of Neuroscience. “Understanding how these traits arose over evolutionary time in icefish may help us to appreciate how similar traits — bone loss, decrease in the ability to make blood cells, problems of the circulatory system, obesity — arise in aging humans over developmental time.”
Researchers collected blackfin icefish, which average about 12 inches long, from various depths near King Sejong Station and the Western Bransfield Strait along the Antarctic Peninsula. Genomic DNA was taken from a single female fish, and RNA was extracted from 12 tissues to help understand what genes each organ uses.
Much of the DNA sequencing was completed by co-author Hyun Park’s group at the Korea Polar Research Institute in Incheon, Korea, and by Wes Warren of Washington University in St. Louis. RNA sequencing and the genetic map of the fish were done in the UO’s research labs and the Genomics and Cell Characterization Core Facility.
The genome assembly and linkage map, the researchers wrote, reveal remarkable stability of contents of the 24 chromosomes among bony fish, including medaka, known as Japanese rice fish; European sea bass; and blackfin icefish spanning 110 million years, especially when compared with chromosome changes in mammals over the same time period. The biggest divergence involved the genes of icefish and sea bass, suggesting changes in the cold.
Icefish and related fish known as notothenioids, which diverged from a stickleback fish ancestor, experienced gene changes that produced antifreeze proteins to help them survive, an adaptation discovered in the 1970s by Arthur DeVries of the University of Illinois at Urbana-Champaign. The genome mapping helps place this gene expansion into a genomic context, the researchers noted.
“Icefish evolved from fish that lived on the bottom and had no swim bladder, an organ that develops like our lungs but then loses the attachment to the pharynx and fills with gas,” Postlethwait said. “Most fish, except for bottom feeders, have one and it helps them maintain position in the water column.”
When most of the fish became extinct around Antarctica as the waters cooled, he said, icefish evolved to occupy the Southern Ocean waters. One of the biggest challenges they faced, he added, was getting off the bottom without a swim bladder.
“They likely limited the mineralization of their bones, the most dense part of our bodies, and accumulated lipids, which are lighter than water. Think of olive oil that floats on the top of the water in a pan about to cook spaghetti,” Postlethwait said.
The new paper was co-authored by a 22-member research team that includes Postlethwait and seven UO colleagues: Angel Amores, Peter Batzel, Julian M. Catchen, Thomas Desvignes, Jason Sydes, Tom Titus and Catherine Wilson. Catchen is now at the University of Illinois.
The other co-authors are with the Korea Polar Research Institute, University of Science and Technology in Daejeon, Korea, Washington University in St. Louis, University of Wuerzburg in Germany, Texas A&M University and Northeastern University in Boston.
The National Institutes of Health and National Science Foundation provided funding for the UO’s role in the research.
