On Thursday, February 19th, the Department of Veterinary Sciences hosted Professor Ted Kalbfleisch from the University of Kentucky. Ted is a Professor of Equine Bioinformatics with deep expertise in genome assembly. He currently leads a multi‑institutional equine pangenome project and has worked on genomes from a wide range of mammals—and even parasites.

Ted opened his talk by emphasizing how quickly genome science has advanced. He noted that over the past few decades, the field has moved from the first human reference genome to producing complete, telomere‑to‑telomere assemblies for many species. According to Ted, T2T genomes are quickly becoming available for an increasing number of animal species.

With sequencing now so accurate and accessible, Ted explained that the major challenge has shifted. Instead of struggling to generate data, researchers must now figure out what all this information means. He described pangenomes as an important step forward because they allow scientists to capture the full range of haplotypes in a species and link them to traits.

The talk also highlighted how dramatically the practical side of genomics has changed. Sequencing and annotating the first mammalian genomes required enormous consortia and millions of dollars. Today, Ted pointed out, a high‑quality genome can be sequenced in just a few days for a few thousand dollars. As sequencing technologies continue to improve—producing longer and more accurate reads—the assembly process becomes far more straightforward.

But these advances also expose the limitations of the traditional reference‑genome approach. Ted reminded the audience that the horse reference genome was built from a Thoroughbred mare named Twilight, kept at Cornell University. Twilight’s genome was invaluable, but as Ted noted, it represents only one individual. When Twilight is used as the reference. any genetic sequence not present in her genome is effectively lost during analysis. He stressed that this problem exists no matter which individual is chosen as the reference.

This is why the equine pangenome is so important. Ted described the pangenome as a combined representation of many individual genomes stacked together, allowing researchers to capture common variation and rare genetic sequences that a single reference would miss. The current equine pangenome includes genomes from 60 horses representing 13 breeds, offering a much broader and more accurate picture of equine genetic diversity.

Compared to the traditional reference‑based approach, the pangenome provides more information at substantially higher quality. As Ted explained, this richer dataset improves our ability to understand the genetic background of both disease and health.

Ted’s talk made clear that genomics has entered a new era. With sequencing no longer the bottleneck, the focus now shifts to interpreting the biology encoded in these complete and diverse genomes. The pangenome approach marks a major step toward that goal.