On Jan. 14, UConn ecology and evolutionary biology associate professor Jill Wegrzyn was among nearly 400 individuals honored by President Biden with the Presidential Early Career Award for Scientists and Engineers (PECASE). This is the highest honor bestowed by the U.S. government on outstanding scientists and engineers who are in the early phases of their careers. UConn engineering professor Arash Zaghi also received this award. 

Established by President Clinton in 1996, PECASE recognizes scientists and engineers who show exceptional potential for leadership early in their research careers. The award celebrates innovative and far-reaching developments in science and technology. 

“This award recognizes Professor Wegrzyn’s exceptional contributions to computational and evolutionary biology, and I am immensely proud of her achievement,” says Ofer Harel, dean of the College of Liberal Arts and Sciences. “Her innovative research pushes the boundaries of genome science and has significant implications for biodiversity conservation.” 

A computational biologist, Wegrzyn develops computational applications for analyzing both single genomes and entire populations, aiming to understand how organisms adapt to their environment. 

“I have always aspired to integrate computer programming and genetics within the broader context of the natural world,” Wegrzyn says.  

This curiosity led to a precocious start to her research career: as an undergraduate at the University of California, Davis, she started to develop some of the university’s first courses in bioinformatics, the study of biological sequence data (like genetic codes). 

Now at UConn, where she leads the Plant Computational Genomics lab, Wegrzyn has worked to develop reference genomes for various “non-model” plant species. In contrast to model organisms, whose genomes have been sequenced and studied extensively, non-model plant species are still genetic mysteries – and many of them are of conservation concern. What’s more, since some of their genomes can be nearly ten times as long as the human genome, effectively sequencing them is no easy task.  

I’m very interested in finding ways to assemble genomes better, faster, and more efficiently, especially when they’re large and complex.

Wegrzyn describes them as the “species that are a little bit harder to work on, and present new computational challenges” — the underdogs of the plant kingdom. 

The lab also works to develop software that can help genomic researchers perform crucial tasks like assembling, analyzing, and annotating genomic data. 

“A lot of the software currently available to tackle those issues has traditionally been very focused on human genetics or model species,” Wegrzyn says. “I’m very interested in finding ways to assemble genomes better, faster, and more efficiently, especially when they’re large and complex. How do we identify genes more efficiently? And how can we scale from working with a single genome to studying entire populations on the landscape, to understand how they’re adapting to a changing climate?” 

This research is assisting conservation efforts for many tree species across the country, which are important for protecting biodiversity and ecosystem health, timber production, and even the nation’s annual Christmas tree crop. 

For example, Wegrzyn says, her lab has identified regions of the genome (genes) that confer resistance to invasive pests or pathogens. Managers can then select for this resistance and plant hardier trees. In the world of forests, where generations are measured not in annual growing cycles but in decades, this could potentially save countless years. 

“Trees can have generation times of 12 to 15 years or more before you can even determine how they’re going to respond to their current (or future) environment,” Wegrzyn says. “So the sooner we can predict how they’re going to perform in a particular environment, the more we can do.” 

The lab is also responsible for creating and maintaining the international CartograPlant database and application, which empowers scientists of all backgrounds to explore how genetics, phenotypes (traits), and environmental factors combine to shape plant population responses. 

Wegrzyn is one of the lead PIs of the NSF-funded Evolving Meta-Ecosystems (EVOME) institute, which seeks to understand how Arctic species (including birds, plants, fish, and insects) will respond, along with their ecosystems, to rapid climate change. 

In addition to her teaching duties and lab research, Wegrzyn is also the Lead Bioinformatician in the Computational Biology Core within the Institute for Systems Genomics. She’s also a PI on UConn’s NSF-funded Research and Mentoring for Postbaccalaureates (RaMP) initiative. RaMP is geared toward recent college graduates who did not have the opportunity to pursue dedicated research as undergraduates, providing them with hands-on lab experience that can culminate in new graduate study or professional opportunities. 

Most recently, RaMP scholars helped generate the first chromosome-level genome of the desert hairy scorpion; this year’s cohort is aiming to do the same with the threatened Everglades mink. 

Wegrzyn became eligible for the PECASE after receiving the NSF’s prestigious CAREER Award in 2020. This award helped fund the development of her EASEL (Efficient, Accurate, Scalable Eukaryotic modeLs) software: an open-source genome annotation tool that leverages machine learning, RNA folding, and functional annotations to enhance gene prediction accuracy. 

“Our software has been applied to everything from deep sea corals to desert invertebrates to high elevation conifers, which represent an incredible range of complexity,” Wegrzyn says. “Through our software, we aim to facilitate fundamental questions in evolution while also providing actionable targets for conservation and restoration programs. Receiving this prestigious award in the midst of climate change elevates the importance of this work and also inspires the students and trainees who contribute to its success.”