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The Irx gene family in zebrafish: genomic structure, evolution and initial characterization of irx5b

Abstract

Genes of the iroquois (Iro/Irx) family are highly conserved from Drosophila to mammals and they have been implicated in a number of developmental processes. In flies, the Iro genes participate in patterning events in the early larva and in imaginal disk specification. In vertebrates, the Irx genes regulate developmental events during gastrulation, nervous system regionalization, activation of proneural genes and organ patterning. The Iro genes in Drosophila and the Irx genes of mammals show a clustered organization in the genome. Flies have a single cluster comprising three genes while mammals have two clusters also having three genes each. Moreover, experimental evidence in flies shows that transcriptional regulatory elements are shared among genes within the Iro cluster, suggesting that the same may be true in vertebrates. To date, the genomic organization of the Irx genes in non-mammalian species has not been studied. In this work, we have isolated the irx5b gene from zebrafish, Danio rerio, and have characterized its expression pattern. Furthermore, we have identified the complete set of Irx genes in two fish species, the zebrafish and pufferfish, Takifugu rubripes, and have determined the genomic organization of these genes. Our analysis indicates that early in fish evolutionary history, the Irx gene clusters have been duplicated and that subsequent events have maintained the clustered organization for some of the genes, while others have been lost. In total there are 11 existing Irx genes in zebrafish and 10 in pufferfish. We propose a new nomenclature for the zebrafish Irx genes based on the analysis of their sequences and their genomic relationships.

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Acknowledgements

We thank Renate Dildrop and Ulrich Rüther for providing a copy of their manuscript prior to publication. X. Wang kindly provided probes. We are also grateful to Peng Jinrong for clone 012-H09-2. We wish to thank Gabino Sánchez-Pérez for help with phylogenetic analysis. Carolina Achondo and Florencio Espinoza provided technical help. C.G.F. and M.A. were supported by grants from Fondecyt (1031003), the ICM (P02-050) and by a grant from the UNAB (DI 10-03). M.M. and J.L.G.-S. were supported by grants from the Spanish Ministry of Science and Technology (BMC2002-03558 and BMC2001-2122, respectively). In addition, M.A. and J.L.G.-S. were supported by a CONICYT-CSIC collaboration grant (2003CL00021).

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Correspondence to Miguel L. Allende.

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Feijóo, C.G., Manzanares, M., de la Calle-Mustienes, E. et al. The Irx gene family in zebrafish: genomic structure, evolution and initial characterization of irx5b . Dev Genes Evol 214, 277–284 (2004). https://doi.org/10.1007/s00427-004-0401-9

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  • DOI: https://doi.org/10.1007/s00427-004-0401-9

Keywords

  • Iroquois
  • Zebrafish
  • Development
  • Gene duplication
  • Teleost