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Last update: May 2021

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National program

The rainbow trout Oncorhynchus mykiss is a widely distributed salmonid species of major importance for both aquaculture and recreational sport fishery. Rainbow trout is also extensively used as a model of investigation in biomedical disciplines as diverse as cancer research, toxicology, comparative immunology, ecology, physiology, nutrition, as well as developmental and evolutionary biology. According to its economic and scientific importance, many genetic and genomic resources have been developed in this species. However, the sequencing of its genome has not been initiated so far, principally due to its respectable size (approximately 0.8x and 6x the size of the human and pufferfish genomes, respectively) and its complexity, with a diploid set of 58-64 chromosomes. This is principally the consequence of an event of tetraploidization (whole genome duplication), which occurred in the salmonid lineage some 25–100 million years ago. Huge costs associated with the classical “Sanger” sequencing of such a large genome have prohibited the initiation of a whole genome sequence project for O. mykiss. The present project, coordinated by scientists affiliated to the French National Institute for Agricultural Research (INRA), aims to take advantage of the new generation sequencing technologies to produce and annotate a draft sequence of the genome of rainbow trout. The sequence itself will be generated and assembled by the French National Sequencing Center Genoscope through a combination of 454-Roche Titanium technology (20x sequence coverage of the genome) and Solexa-Illumina paired reads (50x sequence coverage), in association with a minimal amount of “Sanger” classical sequencing data. Genomic DNA from a totally homozygous double haploid individual will be sequenced, this greatly facilitating the assembly of whole genome shotgun sequences particularly in a context of partial tetraploidy. Such a resource is expected to boost the molecular identification of traits of economical importance in rainbow trout through positional cloning and to allow the development of whole genome marker-assisted selection in breeding programs. The availability of a genome sequence will be also of great benefit for all biomedical disciplines using rainbow trout as a model and will speed up the development of genetics, genomics, transcriptomics and proteomics approaches to tackle many scientific questions in diverse fields of research. Particularly, since salmonids occupy a key position within the tree of life of ray-finned fishes, the availability of rainbow trout genome sequence will very significantly contribute to a better understanding of the structure and evolution of fish genomes and open new avenues for comparative fish genomics. If the Atlantic salmon genome sequence is made available during this project, comparison with the trout genome will allow determining how differential genome rediploidization after tetraploidization contribute to biodiversity and speciation in fish and other organisms. Finally, from a technological point of view, this project will validate new generation sequencing technologies for the de novo sequencing of large and complex genomes.


Inra LPGP, Rennes (Coordinator Yann Guigen)

Genoscope, UMR, CEA, Evry (Olivier Jaillon)

Inra, UMR Génétique Animale et Biologie Intégrative, Jouy-en-Josas (Carine Genêt)

ENS (Institut de Génomique Fonctionnelle de Lyon), Lyon (Jean-Nicolas Volff)