UNM scientist helps international team assemble whale genome
An international team of scientists, including the University of New Mexico’s Dr. Jeremy Edwards, has completely sequenced the minke whale genome, showing its genetic adaption to low oxygen levels, high salt concentration, body hair development, tooth enamel formation, embryonic formation and more.
In a paper published in the November 2013 issue of Nature Genetics, researchers from the Republic of Korea, China, Russia, the United Kingdom, Denmark, Saudi Arabia and the U.S. presented new findings on how whales successfully adapted to an ocean environment. The data improves our understanding of the evolutionary changes required to adapt to inhospitable conditions.
The shift from terrestrial to aquatic life by whales was a significant evolutionary event. In the study, researchers investigated a number of whale-specific genes that were strongly associated with stress resistance to a lack of oxygen and high salt levels. Results reveal gene families associated with stress-responsive proteins and anaerobic metabolism.
Edwards, a UNM professor in the departments of Molecular Genetics and Microbiology, and Chemical Engineering, was instrumental in sequencing the minke whale genome with a deeply layered, highly sophisticated bioinformatics process that exists nowhere else in the world.
UNM has unique capabilities in creating long-sequencing genetic reads of tens-of-thousands of bases – or characters – and accurately stringing them together to create a detailed genomic picture of billions of bases, according to Edwards. “I liken it to reducing the complexity of a 3-billion-piece jigsaw puzzle down to a 1,000-piece puzzle that can be assembled,” he says.
To develop a useful genome, raw sequence data arrive as randomly oriented miniscule slivers, Edwards explains. The technology developed at UNM is able to assign “zip codes” to these genetic slivers and place data in the proper sequence with a high degree of refinement.
“To sequence the genome of a mammal, it takes about a week to construct a sequence library and perform the actual sequencing,” Edwards says. “It takes about a month to identify the specific genes and determine their functions. The subsequent biological analyses take about six months, but a picture emerges about how the whales have evolved to their unique environment."
Compare that to deciphering the human genome, which was 10 years and hundreds of billions of dollars in the making.
“UNM’s capabilities in this arena get us invited to huge international research consortiums,” Edwards adds. “We’re hungry to understand evolutionary adaptation. Genomes evolve to support life under very specific conditions. These studies give us insight to general biological principles, as well as human biology.”
For more information on UNM Health Sciences Center’s Department of Molecular Genetics and Microbiology, visit http://mgm.unm.edu/. To review the full article, visit http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.2835.html.