title: Gene evolution and gene expression after whole genome duplication in fish: the PhyloFish database.
abstract: With more than 30,000 species, ray-finned fish represent approximately half of vertebrates. The evolution of ray-finned fish was impacted by several whole genome duplication (WGD) events including a teleost-specific WGD event (TGD) that occurred at the root of the teleost lineage about 350 million years ago (Mya) and more recent WGD events in salmonids, carps, suckers and others. In plants and animals, WGD events are associated with adaptive radiations and evolutionary innovations. WGD-spurred innovation may be especially relevant in the case of teleost fish, which colonized a wide diversity of habitats on earth, including many extreme environments. Fish biodiversity, the use of fish models for human medicine and ecological studies, and the importance of fish in human nutrition, fuel an important need for the characterization of gene expression repertoires and corresponding evolutionary histories of ray-finned fish genes. To this aim, we performed transcriptome analyses and developed the PhyloFish database to provide (i) de novo assembled gene repertoires in 23 different ray-finned fish species including two holosteans (i.e. a group that diverged from teleosts before TGD) and 21 teleosts (including six salmonids), and (ii) gene expression levels in ten different tissues and organs (and embryos for many) in the same species. This resource was generated using a common deep RNA sequencing protocol to obtain the most exhaustive gene repertoire possible in each species that allows between-species comparisons to study the evolution of gene expression in different lineages. The PhyloFish database described here can be accessed and searched using RNAbrowse, a simple and efficient solution to give access to RNA-seq de novo assembled transcripts.
authors.affiliation: INRA, Laboratoire de Physiologie et Génomique des poissons, Campus de Beaulieu, F-35042, Rennes cedex, France.
authors.forename: Jeremy
authors.initials: J
authors.lastname: Pasquier
authors.affiliation: INRA, SIGENAE, GenPhySE, F-31326, Castanet-Tolosan, France.
authors.forename: Cédric
authors.initials: C
authors.lastname: Cabau
authors.affiliation: INRA, Laboratoire de Physiologie et Génomique des poissons, Campus de Beaulieu, F-35042, Rennes cedex, France.
authors.forename: Thaovi
authors.initials: T
authors.lastname: Nguyen
authors.affiliation: INRA, Laboratoire de Physiologie et Génomique des poissons, Campus de Beaulieu, F-35042, Rennes cedex, France.
authors.forename: Elodie
authors.initials: E
authors.lastname: Jouanno
authors.affiliation: CNRS, MGX-Montpellier GenomiX, Montpellier, France.
authors.forename: Dany
authors.initials: D
authors.lastname: Severac
authors.affiliation: Institute of Neuroscience, University of Oregon, Eugene, 97403-1254, OR, USA.|Department of Integrative Biology, Michigan State University, East Lansing, 48824, MI, USA.
authors.forename: Ingo
authors.initials: I
authors.lastname: Braasch
authors.affiliation: CNRS, MGX-Montpellier GenomiX, Montpellier, France.
authors.forename: Laurent
authors.initials: L
authors.lastname: Journot
authors.affiliation: Aix-Marseille Université, CNRS, Centrale Marseille, I2M, UMR7373, FR 4213 - FR, Eccorev 3098, équipe EBM, 13331, Marseille, France.
authors.forename: Pierre
authors.initials: P
authors.lastname: Pontarotti
authors.affiliation: INRA, SIGENAE, UR 875, MIAT INRA, Toulouse, France.
authors.forename: Christophe
authors.initials: C
authors.lastname: Klopp
authors.affiliation: Institute of Neuroscience, University of Oregon, Eugene, 97403-1254, OR, USA.
authors.forename: John H
authors.initials: JH
authors.lastname: Postlethwait
authors.affiliation: INRA, Laboratoire de Physiologie et Génomique des poissons, Campus de Beaulieu, F-35042, Rennes cedex, France.
authors.forename: Yann
authors.initials: Y
authors.lastname: Guiguen
authors.affiliation: INRA, Laboratoire de Physiologie et Génomique des poissons, Campus de Beaulieu, F-35042, Rennes cedex, France. julien.bobe@rennes.inra.fr.
authors.forename: Julien
authors.initials: J
authors.lastname: Bobe
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods; D030561:Databases, Nucleic Acid; D019143:Evolution, Molecular; D005399:Fishes / Q000145:classification / Q000235:genetics*; D020440:Gene Duplication; D015870:Gene Expression; D020869:Gene Expression Profiling; D016678:Genome; D010802:Phylogeny; D059467:Transcriptome; D064878:Web Browser
keywords: Assembly; Gar; Gene duplication; Gene expression; Holostean; Mcam; Salmonids; Stra8; Teleosts