By Jazmine Robinson
In this installment of our Faces of Innovation series, we sat down with Dr. John Lovell, the leader of the evolutionary analysis group at the Genome Sequencing Center at HudsonAlpha Institute for Biotechnology. His work spans conservation, plant and animal breeding, and cutting-edge genome analysis—melding science, curiosity, and collaboration to tackle some of today’s most complex biological questions. In our conversation, John shares the surprises hidden in genomes, the power of teamwork in science, and his passion for applying genetic insights to real-world challenges like conservation and sustainable agriculture.
Jazmine Robinson: Good afternoon, John. I am so excited to speak with you today and learn more about what you do. Could you briefly explain your role at the institute?
John Lovell: I run the evolutionary analysis group in the Genome Sequencing Center (GSC) at HudsonAlpha Institute for Biotechnology. The GSC is led by Jeremy Schmutz and Jane Grimwood. In genomics, we work to understand the basic DNA sequence that is in every cell in an organism, and combine that with information like “what genes are in what positions” and “how do those genes affect trait variation”. The whole goal of our group is to build state-of-the-art genome resources and apply those to important questions that are asked by our stakeholders. For example, we often work with plant and animal breeders to try to understand the genes that produce proteins that cause useful phenotypic or trait variation, like behaviors in dogs, oil in seeds that are used for biofuels, or growth rate in tall grasses that are feedstocks for cellulosic ethanol.
Jazmine: Have you been surprised by anything that you’ve researched or studied?
John: Every genome that we build and every organism we look at does surprise me in some way. We can think of genomes as being just a simple sequence of A’s, T’s, C’s, and G’s that contain genes and link the cells of that organism to the whole organism’s traits. But often the genomes are absolutely wild, huge, or repetitive, with six or more copies, when you thought there was just one. We have seen genes that have repeated and proliferated across the genome in ways that you would have never imagined. As we see more and more genomes and explore the diversity of organisms, in particular plants, I’m no longer surprised by it anymore. I expect every genome that we build to have a nugget in it that is totally new. The smallest, most compact genome may suddenly have a really crazy centromeric sequence with tons of repeats in it. These are generally surprising, but I think we’re ready for these surprises.
Jazmine: Tell me a little bit more about yourself. For instance, what inspired your interest in pursuing a career in genomics?
John: I think genomics found me — the hardest part of working with experimental big data in biology is presenting a powerful set of results that intuitively support or reject a biological hypothesis. I have a PhD in Ecology, which trained me to integrate diverse experimental approaches and even more diverse data types, and a postdoctoral fellowship in quantitative genetics and data science. The lessons from these fields, and particularly about what makes a persuasive design from complex source data, have set me up for success in genomics.
Jazmine: Do you have any hobbies or interests outside of work?
John: I have a lot of hobbies. I have two little kids, Harrison and Henry. Harrison will be nine this month, and Henry is five. We bike a ton on days like today, where it’s beautiful out. I’ll bike them to and from school. I work remotely from Colorado, and being in Colorado affords a lot of opportunities for outdoor activities like skiing, mountain biking, and hiking, and we really do those as much as we can. My hobbies are really being outside and enjoying what the world has to offer.
Jazmine: What are your long-term aspirations for the field of genetics and genomics?
John: What I really enjoy right now is mentoring the scientists in my group and trying to develop a cohesive team that can tackle any question with any method out there. If someone comes to us with a complicated project or new type of analysis, I want to be able to say, ‘yes, we have experience in a similar system, and that is well within our expertise.’ That’s something that you can’t do as an individual scientist in any field, especially in genomics in particular, because it really does span computer science all the way through to organismal biology. I hope to continue building a team where our collective skill set encompasses all of evolutionary genomics. All of that has been a great motivator for me over the last few years, and makes me very proud right now to really have that in place and be able to answer pretty much any question that could be asked in genomics.
Jazmine: Earth Day was this month. Can you give me an example of how your work benefits society or addresses a specific challenge?
John: One of the things that I am really proud of, and that we do very effectively, is working in the field of conservation biology or conservation genetics. Small isolated populations of plants and animals tend to go extinct because they don’t have the genetic diversity to adapt. This is a ripe field for genomics because genomics is all about understanding the genetic diversity in a system. And if we can combine our expertise with plant breeding and these elements of conservation biology, I think we can make a huge impact.
We have an exciting project in collaboration with the American Chestnut Foundation out of Asheville, North Carolina. The American Chestnut used to be one of the most common species in the Appalachian Mountains from Alabama all the way to Maine. At the turn of the 20th century, different fungal pathogens that were co-adapted with Chinese and Japanese chestnuts arrived in the US and wiped out billions of trees. The chestnuts roasting on the open fire during the holidays have basically gone extinct. We still do that sometimes, but those are European chestnuts that we’re roasting, not an American chestnut, even though that’s a very American story and sentiment.
We set out five or six years ago with the American Chestnut Foundation to build genomic resources for the few standing American chestnut trees and the Chinese and Japanese chestnuts that have evolved to be resistant to these fungal pathogens. The foundation has been trying to breed American chestnut and Chinese chestnut hybrids that look like American chestnut trees and fill that position in the ecosystem with the tolerance and co-adaptation of the Asian species to these invasive pathogens.
I’ve been working with the lead scientist at the American Chestnut Foundation to use genomics to understand what DNA sequences from the Chinese chestnut trees are needed to make a successful American-Chinese hybrid; one that can compete in North American forests, like an American chestnut tree, and is resistant to the invasive pathogens. They’re making huge strides right now based entirely on what we call genomic selection, where you know the DNA sequence of the trees and you can select which ones you want to cross at a very early age. You don’t have to grow thousands of trees up to 10 feet tall. You can just grow a handful of them, knowing their DNA will be compatible. That is one of the projects that’s been most exciting to me, and we’re really close to a publication on that right now.
Jazmine: What advice would you give aspiring researchers or students who are interested in pursuing a career in this field?
John: I suggest first finding a general field that you’re excited about … this is often the biggest challenge. Then work to become an expert at one hard skill, such as an analysis or a wet lab protocol. Eventually, colleagues will come to you for advice on that. In the process of collaborating with others, you will also branch out and learn a lot more. I had no experience in plant breeding. I was a graduate student in ecology, studying native plants, but because I learned one particular analysis that was sometimes used by breeders, I was slowly able to branch out and switch fields.
