UK researchers’ exploration of hagfish genome published in Nature

LEXINGTON, Ky. (April 1, 2024) — A study by a group of researchers at the University of Kentucky in collaboration with scientists in four other countries has been published in the prestigious journal Nature.

Jeramiah Smith, Ph.D., a professor in the Department of Biology in the College of Arts and Sciences, collaborated with an international research group to piece together the hagfish genome and better understand the early evolution of vertebrates.

Their study, “The hagfish genome and the evolution of vertebrates,” was recently published in Nature, which is considered one of the most prestigious and widely respected scientific journals in the world.

Hagfish are a type of jawless fish that typically live in deep ocean waters far from the light of the sun. They are scavengers that play an important role in marine ecosystems. These weird creatures are perhaps best known for their ability to produce huge amounts of slime to protect themselves from predators. Hagfish and lampreys are the only surviving jawless fish.

What do these unusual fish contribute to science? Their genetic material helped researchers like Smith, along with postdoctoral scholars Nataliya Timoshevskaya, Ph.D., and Vladimir Timoshevskiy, Ph.D., piece together a comprehensive picture of vertebrate genome evolution and improve our understanding of how the large collection of genes with our own genomes came to be.

This work expands upon Smith’s previous research on the genome of lampreys, funded by the National Institute of Health’s National Institute of General Medical Sciences and the National Science Foundation.

“In this project, we analyzed the genome of the brown hagfish to help resolve some difficult questions about early vertebrate evolution,” said Smith. “We know it was accompanied by a series of ancient polyploidization events — a genetic change where more than the usual two sets of chromosomes end up in cells.”

In looking at the brown hagfish, researchers were able to resolve new details of genome duplication events, predating the origin of modern vertebrates (animals with a backbone or spinal column) around 500 million years ago, in jawed and jawless vertebrates.

The team of researchers also compared hagfish and lamprey genomes to point out the genetic changes separating the two jawless fish and the unique biology of hagfish.

“Over time, hagfish lost the genes related to developing organs like eyes and cartilage,” said Smith. “However, we saw hagfish have also expanded a few gene families, including slime-producing genes.”   

Because hagfish evolved millions of years ago, Smith said conventional methods to study evolutionary history, or phylogenetics, didn’t give researchers the answers they sought.

“We used the hagfish genome and a new approach focused on chromosome-scale phylogenetics to fully resolve this history of ancient vertebrate polyploidies,” said Smith. “In doing so, we were also able to identify, for the first time, a collection of genes that are also regulated by a natural form of genetic engineering in hagfish ‘programmed DNA elimination’ where some genes are deleted during development.  

“Reconstruction of the early genomic history of vertebrates provides a valuable foundation for understanding where most of the genes in humans and other animals came from, and how genomes work in general,” said Smith. “This research also further explores the evolution of vertebrates and gives us an opportunity to learn more details about our deep ancestry.”

The study brings together researchers from institutions around the world including University College London in the United Kingdom; Okinawa Institute of Science and Technology Graduate University, Shizuoka University and the University of Tokyo in Japan; University of Vienna in Austria; Agency for Science, Technology and Research in Singapore; and University of California, Berkeley, and Chan Zuckerberg Biohub in California.  

The full study in Nature is also published online.

Research reported in this publication was supported by the National Institute of General Medical Sciences of the National Institutes of Health under Award Number R35GM130349. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

Research reported in this publication was supported by the National Science Foundation under Award Number 1818012. The opinions, findings, and conclusions or recommendations expressed are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.