Nav: Home

Oregon research team helps complete genome of Antarctic blackfin icefish

February 25, 2019

EUGENE, Ore. - Feb. 25, 2019 - An international team has unveiled the genome of the Antarctic blackfin icefish, opening a genetic window on fish that evolved over the last 77 million years to survive in temperatures below the freezing point of freshwater.

The research team of 22 scientists, including eight University of Oregon co-authors led by biologist John Postlethwait, published its report Feb. 25 online ahead of print in the journal Nature Ecology & Evolution.

From an adult female, researchers mapped 30,773 protein-coding genes and how they localize along chromosomes. The map points to genes that have adapted or disappeared as the fishes acclimated to rising oxygen concentrations as the Southern Ocean cooled to today's average temperature of a frigid 29 degrees Fahrenheit (-1.67 Celsius).

Blackfin icefish (Chaenocephalus aceratus) is in a family of icefish that has long baffled scientists. They lack functional hemoglobin genes, meaning they are white-blooded and lack the red protein that transports oxygen in the blood of every other animal with a backbone. They exist in a constant state of anemia. They have oversized hearts and a low bone mineral density that makes for floppy spines.

In a human, such traits would normally signal disease. These adaptations, however, help the fish survive, said Postlethwait, professor emeritus of biology and member of the UO's Institute of Neuroscience.

The icefishes, he said, are examples of what Charles Darwin called the "wrecks of ancient life." They diverged from the ancestors of stickleback, losing many of the features common to their ancestral forms as they evolved. Among genes that disappeared amid the months of night and months of sunlight in the polar region were those tied to circadian rhythms. The ways they cope, Postlethwait said, could provide insights into health problems of night-shift workers.

The many adaptations, which also include the ability to manufacture antifreeze proteins, make icefish worthy of extensive study and making comparisons to human health, Postlethwait said.

"We will now be able to mine this genome to learn how the fish evolved these seemingly pathogenic traits to their benefit," Postlethwait said. "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."

Postlethwait raised the idea of studying such adaptations in a species to gain insights into human disease mechanisms and potential new therapies in an article - "Wrecks of Ancient Life": Genetic Variants Vetted by Natural Selection -he wrote for the July 2015 issue of the journal Genetics, soon after he was chosen to receive the George W. Beadle Award from the Genetics Society of America.

In the genome project, researchers collected blackfin icefish, which average about 12 inches in length, from various depths near King Sejong Station and the Western Bransfield Strait along the Antarctic Peninsula. Along with genomic DNA taken from the female, RNA was extracted from 12 tissues - brain, eye, gill, heart, intestine, kidney, liver, muscle, ovary, skin, spleen and stomach - 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 UO research labs and the UO's 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 (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 other notothenioid fishes 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 completed mapping helps place this discovery 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 fish species became extinct around Antarctica as the waters cooled, he said, icefishes evolved to occupy the Southern Ocean water column. 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.
-end-
The new paper was co-authored by a 22-member research team that in addition to Postlethwait includes seven UO colleagues: Angel Amores, Thomas Desvignes, Peter Batzel, Jason Sydes, Tom Titus, Catherine Wilson and Julian M. Catchen. 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 project was funded by grants from the National Institutes of Health, National Science Foundation, Korea Polar Research Institute Polar Genome 101 Project, German Research Foundation and Hagler Institute of Advanced Study at Texas A&M University.

Media Contact: Jim Barlow, director of science and research communications, 541-346-3481, jebarlow@uoregon.edu

Source: John Postlethwait, professor emeritus, Department of Biology, member of Institute of Neuroscience, University of Oregon, 541-346-4538, jpostle@uoregon.edu

Note: The UO is equipped with an on-campus television studio with a point-of-origin Vyvx connection, which provides broadcast-quality video to networks worldwide via fiber optic network. There also is video access to satellite uplink and audio access to an ISDN codec for broadcast-quality radio interviews.

Links:

About John Postlethwait: https://ion.uoregon.edu/content/john-postlethwait

UO Department of Biology: https://biology.uoregon.edu/

UO Institute of Neuroscience: https://ion.uoregon.edu/

2015 Genetics Paper: http://www.genetics.org/content/200/3/675

University of Oregon

Related Genome Articles:

A close look into the barley genome
An international consortium, with the participation of the Helmholtz Zentrum München, Plant Genome and Systems Biology Department (PGSB), has published methodologically significant data on the barley genome.
Barley genome sequenced
Looking for a better beer or single malt Scotch whiskey?
From Genome Research: Pathogen demonstrates genome flexibility in cystic fibrosis
Chronic lung infections can be devastating for patients with cystic fibrosis (CF), and infection by Burkholderia cenocepacia, one of the most common species found in cystic fibrosis patients, is often antibiotic resistant.
A three-dimensional map of the genome
Cells face a daunting task. They have to neatly pack a several meter-long thread of genetic material into a nucleus that measures only five micrometers across.
Rhino genome results
A study by San Diego Zoo Global reveals that the prospects for recovery of the critically endangered northern white rhinoceros -- of which only three individuals remain -- will reside with the genetic resources that have been banked at San Diego Zoo Global's Frozen Zoo®.
Science and legal experts debate future uses and impact of human genome editing in Gender & the Genome
Precise, economical genome editing tools such as CRISPR have made it possible to make targeted changes in genes, which could be applied to human embryos to correct mutations, prevent disease, or alter traits.
Genome: It's all about architecture
How do pathogens such as bacteria or parasites manage to hide from their host's immune system?
Accelerating genome analysis
An international team of scientists, led by researchers from A*STAR's Genome Institute of Singapore and the Bioinformatics Institute, have developed SIFT 4G (SIFT for Genomes) -- a software that can lead to faster genome analysis.
Packaging and unpacking of the genome
Single-cell techniques have been used to investigate histone replacement and chromatin remodeling in developing oocytes.
The astounding genome of the dinoflagellate
Dinoflagellates live free-floating in the ocean or symbiotically with corals, serving up -- or as -- lunch to a host of mollusks, tiny fish and coral species.

Related Genome Reading:

Best Science Podcasts 2019

We have hand picked the best science podcasts for 2019. Sit back and enjoy new science podcasts updated daily from your favorite science news services and scientists.
Now Playing: TED Radio Hour

Setbacks
Failure can feel lonely and final. But can we learn from failure, even reframe it, to feel more like a temporary setback? This hour, TED speakers on changing a crushing defeat into a stepping stone. Guests include entrepreneur Leticia Gasca, psychology professor Alison Ledgerwood, astronomer Phil Plait, former professional athlete Charly Haversat, and UPS training manager Jon Bowers.
Now Playing: Science for the People

#524 The Human Network
What does a network of humans look like and how does it work? How does information spread? How do decisions and opinions spread? What gets distorted as it moves through the network and why? This week we dig into the ins and outs of human networks with Matthew Jackson, Professor of Economics at Stanford University and author of the book "The Human Network: How Your Social Position Determines Your Power, Beliefs, and Behaviours".