Euteleost Fish Genomes are Characterized by Expansion of Gene Families
- Marc Robinson-Rechavi1,3,4,
- Oriane Marchand1,3,
- Héctor Escriva1,
- Pierre-Luc Bardet1,
- Dominique Zelus1,
- Sandrine Hughes2, and
- Vincent Laudet1
- 1Centre National pour la Recherche Scientifique UMR 5665, Laboratoire de Biologie Moléculaire et Cellulaire, Ecole Normale Supérieure de Lyon, 46 Alleé d'Italie 69364 LYON Cedex 07, France; 2CNRS UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Université Claude Bernard Lyon 1, 69622 Villeurbanne Cedex, France
Abstract
The presence of additional hox clusters in the zebrafish has led to the hypothesis that there was a whole genome duplication at the origin of modern fish. To investigate the generality of this assumption, we analyzed all available actinopterygian fish gene families, and sequenced nuclear receptors from diverse teleost fish. The origin and timing of duplications was systematically determined by phylogenetic analysis. More genes are indeed found in zebrafish than in mouse. This abundance is shared by all major groups of euteleost fish, but not by eels. Phylogenetic analysis shows that it may result from frequent independent duplications, rather than from an ancestral genome duplication. We predict two zebrafish paralogs for most mouse or human genes, thus expressing a note of caution in functional comparison of fish and mammalian genomes. Redundancy appears to be the rule in fish developmental genetics. Finally, our results imply that the outcome of genome projects cannot be extrapolated easily between fish species.
