Salmon and trout study aids insights on extreme DNA duplication event

A study of salmon and trout has revealed how gene functional activity changed following a complete duplication of their ancestors’ genetic material around 100 million years ago, an article on Stirling University's website reports.

The findings uncover the long-term impacts of whole genome duplication, a key event in evolution where the complete DNA code doubles, subsequently giving rise to new genes and biological functions across millions of years.

Data and methodologies developed in the study will aid research into commercially important fish species and fundamental aspects of gene evolution in many other species.

A team of experts led by the Roslin Institute at the University of Edinburgh and the Norwegian University of Life Sciences, generated a large dataset in two species, Atlantic salmon and rainbow trout, to investigate processes that control when and where genes are switched on in different cell types and tissues.

The data, derived from samples taken from fish at varying stages of development and adulthood, included details from genes present before and after a whole genome duplication event, which occurred in the ancestor to salmon and trout about 100 million years ago.

Evolutionary processes

Researchers found that the evolution of gene expression following whole genome duplication is constrained by developmental processes that exist across many species, including humans.

They examined the point of development where embryos of all animals with backbones closely resemble one another, known as the phylotypic stage. This stage was found to mark the point of greatest similarity in gene activity across duplicated parts of the genome, casting light on a fundamental aspect of evolutionary biology.

The study, published in the journal Nature Ecology and Evolution, involved collaborating organisations across the UK and Europe.

All data and new methods have been openly shared by the research team, to support further studies of fish biology and fundamental evolution.

Improved understanding

Study lead Dan Macqueen, professor of integrative fish genomics at the Roslin Institute, said: “Salmonids doubled their genome 100 million years ago, and half their current genes were retained in duplicated copies in the aftermath. However, how these new genes evolved has remained poorly understood.

“Our study improves understanding of changes in gene regulation that follow genome duplication, which has relevance to many lineages in the tree of life that similarly duplicated their whole DNA, for example our deep vertebrate ancestors.”

Dr Rose Ruiz Daniels, lecturer in aquaculture genomics at Stirling University’s Institute of Aquaculture, took part in the study.

“Playing a small role in such a big study has been a privilege,” said Daniels.

“Above all, this work is a testament to collaboration and perseverance in trying to understand how genomes function: how gene expression is regulated and how that regulation is affected by genome duplication. This is especially important for understanding salmonids and how we can farm and conserve them better.”

Developmental contexts of gene-regulatory evolution following whole genome duplication in salmonids is published in Nature.