Watson, who works in the Department of Biochemistry and Molecular Genetics, School of Medicine, focuses on comparative genomics and immunology, also known as immunogenomics. This expertise earned a place on a multidisciplinary team led by Penn State, Washington University and the who recently generated the first : chimpanzee, bonobo, gorilla, Bornean orangutan, Sumatran orangutan and siamang. Watson, and members of his lab team assisted in undertaking the large project, utilizing their niche expertise to help identify and analyze the ape genes related to immunity. 

The ape genome findings published in help scientists better understand species-specific genes that may have played a role in the species’ survival and development. Geneticists like Watson are discovering the narrative of evolution by studying and translating genomes into actionable information. Genomic differences between humans and our close genetic relatives may direct future advancements in understanding human health and clinical research.

“I like to think that when you understand more about the biology of these regions, you understand more about how they can be useful to humans in the health setting,” Watson said.

Piecing together the ape genome puzzle

The complete sequencing of the six ape genomes revealed novel genes and variants related to diet, immunity and cellular activity. 

“The regions that harbor antibody genes are very complex parts of the genome, and we still actually don’t understand them that well, even in humans,” Watson said. “We don’t know much about their evolutionary histories. While we now understand they are places in our genome that have very particular characteristics, we lack a clear understanding of how quickly they can diversify and take on new functions within and between species.”

The complete genomes of the six ape species have been sequenced thanks to technological advancements that have made genomic sequencing cheaper and more efficient. However, the process for sequencing a genome is not as simple as running it through a single computer program, as seen in sci-fi movies like “Jurassic Park.” Watson describes the sequencing process as similar to completing a jigsaw puzzle. Laboratory researchers break up chromosomes into small pieces of DNA, analyze them and put them back together to understand the whole. 

“We’re now to the point where — with a lot of effort through the input of a lot of people — we can fully reconstruct genomes, and it doesn’t cost you a billion dollars to do it,” Watson said, referring to the rough cost of the original of the early 2000’s. 

Technological developments have allowed today’s researchers to analyze much larger DNA pieces, so the change in sequencing difficulty is like having fewer pieces of a puzzle to put together.

Despite the progress, this work remains an intense process requiring experts like Watson, who helped identify and describe the ape genes that contribute to immune responses. For the Watson Lab and other immunogenomic researchers, future advancement in our genetic understanding of immunity will require sequencing of many more individual apes and humans to better identify gene variations across these species.

Students are critical to the research

Watson and his team were just one branch of a large team of scientists piecing together and organizing the jigsaw of the six ape genomes. The amount of work needed in genetics to sequence, annotate and store genetic information is great, which leaves space for rising biology students. 

“Students are critical to our research enterprise. All of us were once students; it’s where you start,” Watson said, regarding the future of genetic studies. “The future of the system we have built in this country wholly depends on our ability to continue to recruit and effectively train students who are interested in scientific research.”

For Watson and his team of UofL researchers, the work to understand the genetic story of humans’ adaptive immune system continues with more of our close relatives. The Watson Lab recently completed . The study included a curated public database of more than 1,000 previously unidentified alleles and is available with the team’s January 2026 article published in .

Watson, along with UofL post-doctoral fellow Oscar Rodriguez, and visiting fellow Yana Safonova, are part of an international group of researchers who say the narrow studies limit their ability to identify variation in human adaptive immune responses across populations.

“We need to better understand how genetics influences immune system function by studying population cohorts that better represent the diversity observed across the globe if we are to fully understand disease susceptibility, as well as design more tailored treatments and preventative measures,” Watson said.

In an article published in Nature Methods, , the group advocates for resources used in immunogenomics research to actively include and specifically identify additional populations and minority groups. They say such diversity will make their research more relevant and help in understanding population and ancestry-specific gene-associated disease, leading to improvements in patient care.

“As scientists, we have a say in which populations are investigated. Therefore, it is critical for us to be actively inclusive of individuals representative of the world we live in. This is especially critical for genes that are as diverse and clinically relevant as those that encode antibodies and T cell receptors,” Rodriguez said.

Watson’s research focuses on immune function and molecular genetics. His team is studying a specific area of the genetic code that controls antibody function to better understand how differences in an individual’s genes determine their susceptibility to certain diseases or immune responses to vaccines.

In collaboration with Melissa Smith, assistant professor in the , the team is conducting the largest sequencing efforts of the antibody gene regions in humans and in animal models, Watson said.

“Specifically in humans, we are working to build catalogs of genetic variation in samples from multiple ethnic backgrounds and are engaged in projects that seek to understand how this genetic variation influences the immune response in infection, vaccination and other disease contexts,” he said.

Watson is involved in efforts to improve the resources and data standards for antibody and T cell receptor genes for immunogenomics researchers around the world.

The article in Nature Methods was co-authored by researchers from the United States, Canada, Norway, France, Sweden, the United Kingdom, Russia, Saudi Arabia, Israel, South Africa, Nigeria, Chile, Peru, China, Japan, Taiwan and French Polynesia with expertise in biomedical and translational research, population and public health genetics, health disparities and computational biology as well as immunogenomics.