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

• Published in: Genome research 2004-01, Vol.14 (1), p.11-17
• Main Authors: Chiu, Chi-hua, Dewar, Ken, Wagner, Günter P., Takahashi, Kazuhiko, Ruddle, Frank, Ledje, Christina, Bartsch, Peter, Scemama, Jean-Luc, Stellwag, Edmund, Fried, Claudia, Prohaska, Sonja J., Stadler, Peter F., Amemiya, Chris T.
• Format: Article
• Language: English
• ISSN: 1088-9051
• DOI: 10.1101/gr.1712904

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 Hox A cluster of the bichir ( Polypterus senegalus ), a phylogenetically basal actinopterygian. Independent lines of evidence indicate that bichir has one Hox A cluster that is mosaic in its patterns of noncoding sequence conservation and gene retention relative to the Hox A clusters of human and shark, and the Hox Aα and Hox Aβ clusters of zebrafish, pufferfish, and striped bass. Hox A 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 Hox A cluster was already more dynamic than in human and shark. This tendency peaked among teleosts after Hox A cluster duplication.