RT Journal
A1 Chiu, Chi-hua
A1 Dewar, Ken
A1 Wagner, Günter P.
A1 Takahashi, Kazuhiko
A1 Ruddle, Frank
A1 Ledje, Christina
A1 Bartsch, Peter
A1 Scemama, Jean-Luc
A1 Stellwag, Edmund
A1 Fried, Claudia
A1 Prohaska, Sonja J.
A1 Stadler, Peter F.
A1 Amemiya, Chris T.
T1 Bichir HoxA Cluster Sequence Reveals Surprising Trends in Ray-Finned Fish Genomic Evolution
JF Genome Research 
JO Genome Research 
YR 2004 
FD January 01 
VO 14 
IS 1 
SP 11 
OP 17 
DO 10.1101/gr.1712904 
UL http://genome.cshlp.org/content/14/1/11.abstract 
AB 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.