title: Bichir HoxA cluster sequence reveals surprising trends in ray-finned fish genomic evolution.
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 HoxAalpha and HoxAbeta 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.
authors.affiliation: Department of Genetics, Rutgers University, Piscataway, New Jersey 08854, USA. chiu@biology.rutgers.edu
authors.forename: Chi-Hua
authors.initials: CH
authors.lastname: Chiu
authors.forename: Ken
authors.initials: K
authors.lastname: Dewar
authors.forename: Günter P
authors.initials: GP
authors.lastname: Wagner
authors.forename: Kazuhiko
authors.initials: K
authors.lastname: Takahashi
authors.forename: Frank
authors.initials: F
authors.lastname: Ruddle
authors.forename: Christina
authors.initials: C
authors.lastname: Ledje
authors.forename: Peter
authors.initials: P
authors.lastname: Bartsch
authors.forename: Jean-Luc
authors.initials: JL
authors.lastname: Scemama
authors.forename: Edmund
authors.initials: E
authors.lastname: Stellwag
authors.forename: Claudia
authors.initials: C
authors.lastname: Fried
authors.forename: Sonja J
authors.initials: SJ
authors.lastname: Prohaska
authors.forename: Peter F
authors.initials: PF
authors.lastname: Stadler
authors.forename: Chris T
authors.initials: CT
authors.lastname: Amemiya
mesh_terms: D000818:Animals; D001482:Base Composition / Q000235:genetics; D021901:DNA, Intergenic / Q000235:genetics; D005801:Genes, Homeobox / Q000235:genetics; D016678:Genome; D018398:Homeodomain Proteins; D006801:Humans; D005810:Multigene Family / Q000235:genetics*; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D012860:Skates, Fish / Q000235:genetics*; D015534:Trans-Activators / Q000235:genetics*
chemical_list: D021901:DNA, Intergenic; D018398:Homeodomain Proteins; D015534:Trans-Activators; C088144:HoxA protein