Genome sequencing yields largest database of genetic variations for nonhuman primates

BATON ROUGE—LSU College of Science researchers have contributed to a genome sequencing research project that has yielded the largest database of genetic variations for nonhuman primates. 

Published in the journal Science, the paper, “Sequence diversity analyses of an improved rhesus macaque genome enhance its biomedical utility,” establishes a new long-read reference genome assembly and identifies more than 85 million genetic variants in the rhesus macaque, the largest database of genetic variation for any one nonhuman primate species to date.

“What this does is it allows us to take a nonhuman primate model and—using more accurate information about the variation or the genetic changes within the sequence—we can begin to develop new models of human genetic disease and also gain better insight into the evolution of nonhuman primates,” said Dr. Mark Batzer, LSU Boyd Professor and the Dr. Mary Lou Applewhite Distinguished Professor in the Department of Biological Sciences.

Batzer, along with members of the Batzer Laboratory of Comparative Genomics Jerilyn A. Walker, staff scientist, and Jessica M. Storer, recently graduated doctoral student, contributed to the research through the transposable element or mobile element related analyses.

The mobile elements are components of the genome that are otherwise known as transposable elements—or “junk.” The researchers looked at how some of these elements evolved through time (Figure 4) and in response to different repressors of their mobility in collaboration with UC Santa Cruz’s Dr. Jason Fernandes (seen in Figure 5), as well as the evolution that has gone on in an attempt to mitigate their mobilization.

And these mobile elements—or junk—make up a big part of our genome. They come in two groups, with each having hundreds of thousands—if not a million—members, collectively making up greater than a quarter of our genomes. 

“For the most part, the elements are innocuous—they don’t have any function—but occasionally, as these elements move around in the genome, they can cause a new detrimental mutation. About 1 percent of all human genetic mutations are the result of mobile element mediated mutations,” Batzer said.

Old World monkeys represent biomedical models that are also closely related non-human primates. The rhesus macaque (Macaca mulatta) is a widely dispersed nonhuman primate species that diverged from the ancestors of Homo sapiens about 25 million years ago. As a representative of the Old World monkey lineage, the rhesus macaque’s genetic sequence is critical for studies of primate evolution. It’s also one of the most widely used nonhuman primate models for studying human biology and disease.

The researcher explained, macaques are often used to understand viral infections, how to resist them, and how to develop vaccines to treat the viruses. While these studies largely focus on the human immunodeficiency virus, or HIV, “they’ve also had some utility in COVID related studies,” Batzer explained.

For a full list of authors and funding, see the publication.

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