Bichir HoxA Cluster Sequence Reveals Surprising Trends in Ray-Finned Fish Genomic Evolution

  1. Chi-hua Chiu1,2,13,
  2. Ken Dewar3,
  3. Günter P. Wagner4,
  4. Kazuhiko Takahashi4,
  5. Frank Ruddle5,
  6. Christina Ledje6,
  7. Peter Bartsch7,
  8. Jean-Luc Scemama8,
  9. Edmund Stellwag8,
  10. Claudia Fried9,10,
  11. Sonja J. Prohaska9,10,
  12. Peter F. Stadler9,10,11, and
  13. Chris T. Amemiya12
  1. 1 Department of Genetics, Rutgers University, Piscataway, New Jersey 08854, USA
  2. 2 Center for Human Evolutionary Studies, Department of Anthropology, Rutgers University, New Brunswick, New Jersey 08901, USA
  3. 3 Department of Human Genetics, McGill University, Montreal, Quebec H3A1A4, Canada
  4. 4 Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520, USA
  5. 5 Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA
  6. 6 Department of Genetics, University of Lund, SE-223, Sweden
  7. 7 Museum für Naturkunde der Humboldt-Universität zu Berlin, D-10099 Berlin, Germany
  8. 8 Department of Biology, Howell Science Complex, East Carolina University, Greenville, North Carolina 27858, USA
  9. 9 Bioinformatics, Department of Computer Science, University of Leipzig, D-04103 Leipzig, Germany
  10. 10 Institute for Theoretical Chemistry and Structural Biology, University of Vienna, A-1090 Wien, Austria
  11. 11 The Santa Fe Institute, Santa Fe, New Mexico 87501, USA
  12. 12 Benaroya Research Institute at Virginia Mason, Seattle, Washington 98101, USA

Abstract

The study of Hox clusters and genes provides insights into the evolution of genomic regulation of development. Derived ray-finned fishes (Actinopterygii, Teleostei) such as zebrafish and pufferfish possess duplicated Hox clusters that have undergone considerable sequence evolution. Whether these changes are associated with the duplication(s) that produced extra Hox clusters is unresolved because comparison with basal lineages is unavailable. We sequenced and analyzed the HoxA cluster of the bichir (Polypterus senegalus), a phylogenetically basal actinopterygian. Independent lines of evidence indicate that bichir has one HoxA cluster that is mosaic in its patterns of noncoding sequence conservation and gene retention relative to the HoxA clusters of human and shark, and the HoxAα and HoxAβ clusters of zebrafish, pufferfish, and striped bass. HoxA cluster noncoding sequences conserved between bichir and euteleosts indicate that novel cis-sequences were acquired in the stem actinopterygians and maintained after cluster duplication. Hence, in the earliest actinopterygians, evolution of the single HoxA cluster was already more dynamic than in human and shark. This tendency peaked among teleosts after HoxA cluster duplication.

Footnotes

  • [Supplemental material is available online at www.genome.org.]

  • Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.1712904.

  • ↵13 Corresponding author. E-MAIL chiu{at}biology.rutgers.edu; FAX (732) 445-1147.

    • Accepted October 30, 2003.
    • Received July 1, 2003.
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  1. doi: 10.1101/gr.1712904 Genome Res. 14: 11-17 Cold Spring Harbor Laboratory Press

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