GENOM-BTV - Génomique, Biotechnologies végétales

RNASeq-based PHYLOgenomic analysis of gene duplications in teleost FISHes – PhyloFish

Evolution of the repertoire of expressed genes in teleost fish

Evolution of the repertoire of expressed genes in teleost, impact of whole genome duplication and evolutionary-supported gene annotation.

A comprehensive view of expressed genes in teleost fish

Teleost fish represent more than half of the total number of vertebrate species. Among the 30000 species of teleost fish, only a limited number of genomes are available, mostly in species that are phylogenetically relatively close. In addition, teleost fish have been subjected to several rounds of whole genome duplications since their radiation 300-350 million years ago. This further complicates molecular studies and gene annotation in a group of species of major economical and environmental interest. The project aims at studying gene evlution within teleosts and to provide evolutionary-based automatic gene annotation. In addition to the thorough analysis of new gene function after duplication, the projet will also yield significant amounts of new genomic ressources in several species of major economical and environmental interest.

A total of 10 tissues or organs have been collected from more than 20 different teleost species and corresponding RNA subjected to deep next-generation sequencing using the illumina technology. This was also performed in 2 holostean species that did not undergo whole genome duplication, in contrast to teleosts. A de novo assembly was performed in each studied species and used to obtain coding sequence of expressed genes in the anlayzed tissues/organs of each studied species. An automatic phylogenetic analysis was subsequently carried out in order to thoroughly analyze the evolutionary history of corresponding genes and to provide evolutionary-supported gene annotation.

The project has already yielded a significant amount of new genomic ressources in more than 20 species including species of major economical and environmental interest such as European eel, European perch, Northern pike, Alice shad, panga, Atlantic cod as wel as 7 salmonid species. In most of those species, existing genomic ressources were scarce and the project will significantly increase both molecular analysis possibilities and corresponding biotechnological applications.

After a first step of sample collection and subsequent sequencing of almost 250 tissue- libraries, we have been able to generate, on average, 27000 assembled sequences corresponding to expressed genes in each studied species. These sequences are currently used to thoroughly characterize the evolutionary history of expressed genes in teleosts with special interest for gene evolution after whole genome duplication.

Bobe J, Westerfield M, Pontarotti P, Klopp C, Journot L, Postlethwait J, Guiguen Y. Gene annotation with evolutionary support in teleosts with a focus on the salmonid lineage. First International Conference on the Integrative Biology of Salmonids, Oslo 17

Genome duplication is a recurring theme in vertebrate evolution and for instance, the human genome still contains numerous gene families that arose from the two rounds of genome duplication at the origin of vertebrates. Teleost fish are in that regards very interesting models due to an additional whole genome duplication (WGD) event that occurred at the base of their radiation, resulting in duplicated copies of many single-copy human genes. These ‘extra’ genes are, in principle, available for the evolution of new functions that could drive the origin of novelties and thus contribute to the diversification of life on Earth. Gene evolution after genome duplication is thus a crucial question to understand the mechanisms by which genomes evolved and drive the development and physiology of vertebrates. Unfortunately, we still do not yet have a sufficient understanding of vertebrate genomes to fully answer this question. The present project will make use of the additional WGDs of teleosts to address this question. By using next generation sequencing this project will first provide novel and genome-wide information on the transcript repertoires of different fish species chosen at key taxonomic positions with regards to teleost fish evolution. This evolutionary-relevant sequence dataset will then be used as a basis for the development of a high throughput analysis combining gene phylogenies, conserved syntenies and expression profiling. Results of this project should provide genome-wide answers on how often different gene copies are lost independently in different fish lineages and whether lineage-specific changes in duplicate gene content or in expression patterns of duplicated genes is important for the evolution of the remarkable diversity among teleosts. In addition and because these gene duplications also have a major impact on the quality of gene annotation in teleosts, this project will propose, supported by the results of our evolutionary-based analysis, the refinement of teleost gene nomenclature. This will link gene information across many vertebrate species, allowing to bridge functional information from model species to economically-relevant species.

Project coordinator

INSTITUT NATIONAL DE LA RECHERCHE AGRONOMIQUE - CENTRE DE RECHERCHE DE RENNES (Divers public)

The author of this summary is the project coordinator, who is responsible for the content of this summary. The ANR declines any responsibility as for its contents.

Partner

INSTITUT NATIONAL DE LA RECHERCHE AGRONOMIQUE - CENTRE DE RECHERCHE DE RENNES
CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE - DELEGATION REGIONALE LANGUEDOC-ROUSSILLON
INSTITUT NATIONAL DE LA RECHERCHE AGRONOMIQUE -CENTRE DE RECHERCHE DE TOULOUSE
UNIVERSITE AIX-MARSEILLE I [DE PROVENCE]

Help of the ANR 481,356 euros
Beginning and duration of the scientific project: - 48 Months

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