Trout genome sequencing redefines the evolution of vertebrate genomes

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A French consortium, coordinated by INRA and gathering CEA (Genoscope), CNRS and the Ecoles Normales Supérieures of Paris and Lyon, sequenced and analyzed the genome of the rainbow trout (Oncorhynchus mykiss), which constitutes the first published genome of a salmonid (salmons and trouts family). This sequence, published on April 22, 2014 in Nature Communications, introduces a new scenario for the evolution of vertebrate genomes and opens up new prospects for selection in aquaculture.

The rainbow trout is an important aquaculture species bred all around the world. It belongs to the salmonid family, of which numerous species are of major agronomical and ecological interest. The trout is also a model for research and the most studied fish. It is the first time a complete genome sequence is published for a salmonid.

A precious resource for genome evolution

This sequence gives new insights into the evolution of vertebrate genomes. Complete genome duplications are events that profoundly molded the content and structure of genomes, including the human genome. Unfortunately, the mechanisms underlying the evolution of a genome after such an event happens are not well understood in animals, and in particular the steps taking place in the tens of millions of years following duplication.

The rainbow trout is in this matter a particularly interesting species as its genome has been completely duplicated relatively recently (100 million years ago), in the common ancestor of all current salmonids. The surprising conclusion of this study is that the evolution of vertebrate genomes after full duplication is a slow and gradual process. Despite the 100 million years that passed since this event, the two copies remain well conserved. Not only the general structure of the two copies remained similar, but the content in genes is highly conserved, and many of the ancestral genes are still there and functional. This result calls into question the commonly accepted hypothesis that the evolution of a genome following a complete duplication implies a rapid evolution of its structure and gene content.

Outcomes in aquaculture

This sequence opens up great perspectives in the development of a more efficient and sustainable aquaculture, by accelerating the analysis of important breeding traits, the identification of genes and the implementation of selection programs that are more efficient.

The project was sponsored by a grant from the Agence nationale pour la recherche (ANR Genotrout, ANR-09-GENM-001 “Plant Genomics and Biotechnologies”)

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