REWIRED ─ The role of whole genome duplication in vertebrate adaptation

REWIRED ─ The role of whole genome duplication in vertebrate adaptation

Evolution

In the REWIRED project, we will use salmonid fish, which underwent a genome duplication 100 million years ago, as a model system to study the importance of genome duplication in evolution of new gene functions and adaptation.

prosjekt

About/Aims
Background

The premise for all natures magnificent variation in species, life strategies and adaptations is differences in the DNA code. These genetic differences can be traced back to the sequence of the code, how DNA is organized into chromosomes and, ultimately, how the code is used to produce proteins in each cell type. Hence, if we wish to understand how new adaptations and species arise, we need to understand how new DNA-variation arise through mutations and how these novel variations in the DNA-code gives rise to new functions. One spectacular way that the DNA can change from one generation to the next is through spontaneous doubling of all chromosomes – a whole genome duplication. Each gene gets a copy of itself on a different chromosome. This type of mutational event is of course rare, but can have large consequences for evolution of new traits and species. A central hypothesis within the field of evolutionary biology is that genome duplications spark evolution of novel adaptations. The idea is intuitive: one gene copy can maintain its original function while the other copy is free to accumulate mutations and change function. This speed up generation of novel genetic variants – the very basis for evolutionary change. However, the link between whole genome duplication and adaptation has so far not been empirically tested.

Objectives

Primary objective:

  • Assess the role of whole genome duplications (WGD) as catalysts for adaptive evolution in vertebrates

Secondary objectives:

  • SO1: Identify targets (i.e. genes) for adaptive regulatory evolution following vertebrate WGDs
  • SO2: Understand the mechanistic basis for evolution of gene regulation following WGD
  • SO3: Experimentally validate the adaptive nature of novel functions arising from WGD
More about the project

To do this we will generate large amounts of gene regulation data using DNA and RNA sequencing across different organs in eight species of salmonid fish. Next we will utilize novel statistical methods and bioinformatics to compare the evolution of gene regulation after whole genome duplication with that of the distant fish-cousins that have not undergone the same genome duplication. This comparative dataset can then be used to infer if genome duplication leads to increased rates of evolution of new adaptive gene functions.

Finally, we will put the results from the computational analyses to the test using state-of-the-art gene editing technology (CRISPR). By deleting gene duplicates from the genome of Atlantic salmon we can measure what consequences this has on fish physiology and function. The project will focus on new gene functions related to liver lipid metabolism as we can keep small pieces of liver alive in petri dishes for several weeks. This enables us to “feed” the same liver lipid poor and rich diets and characterize in detail how the liver function is changed when a duplicate gene is removed.

The results from REWIRED will provide new understanding of how the most extreme form of DNA mutation – genome duplications – shape the evolution of new traits and adaptations.

 

Norwegian University of Life Sciences (NMBU)

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