Ingo Braasch, PhD – Michigan State University — CSB Seminar

CSB Departmental Seminar

Friday, December 5th @ 11:00 am

SPEAKER: Ingo Braasch, PhD – Michigan State University

TITLE: A Blast From the Past: ‘Living Fossils’ Bridge Gene Regulation Across Long Evolutionary Distances in Vertebrates

ABSTRACT: Identifying cis-regulatory elements (CREs) across distant vertebrate lineages remains a major challenge. Many CREs are undetectable across taxa due to sequence divergence beyond recognition, CRE turnover, and the emergence of lineage-specific regulatory elements. This disconnect is especially pronounced in widely used model systems like rodents and teleost fishes, which exhibit rapid molecular sequence evolution.
Teleosts, including key biomedical models like zebrafish, are often used to study vertebrate genome function and regulation. However, a lineage-specific teleost genome duplication (TGD) drastically reshaped their genome structure and regulatory networks. Their accelerated sequence evolution, likely driven by the TGD, has obscured many ancestral CREs, complicating efforts to trace the evolution of gene regulation across vertebrates.
In contrast, holostean fishes – gars (genera Lepisosteus and Atractosteus) and bowfins (genus Amia) – retain some of the slowest-evolving genomes among vertebrates. These “living fossils” provide a unique window into early bony vertebrate evolution. Their unduplicated genomes, conserved development, and archaic morphologies offer critical insight into deep homologies that have been masked by rapid evolution in the derived teleost and tetrapod lineages.
Leveraging haplotype-resolved genome assemblies from multiple holostean species we use comparative genomics, single-cell transcriptomics, and epigenomic profiling in holosteans to reveal ancestral CREs and recover hidden gene regulatory landscapes across bony vertebrates. The evolutionary stability of holostean genomes enables the identification of conserved vertebrate CREs that would otherwise remain hidden for fast-evolving taxa. Our work underscores the immense value of including slow-evolving lineages across the Vertebrate Tree of Life to reconstruct the deep history of gene regulation and uncover the genome regulatory logic that shapes vertebrate biodiversity.

HOST: Max Shafer

LOCATION: Cell and Systems Biology, 25 Harbord Street, Suite 432

LIVESTREAM LINK: https://csb.utoronto.ca/live-stream/