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
Department of Genetics, Rutgers University, Piscataway, New Jersey 08854, USA.
Genome Res. 2004 Jan;14(1):11-7. 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 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.
对Hox基因簇和基因的研究为发育的基因组调控进化提供了见解。像斑马鱼和河豚这样的衍生硬骨鱼（辐鳍鱼纲，真骨鱼类）拥有经过大量序列进化的重复Hox基因簇。由于无法与基部谱系进行比较，这些变化是否与产生额外Hox基因簇的重复相关尚不清楚。我们对多鳍鱼（塞内加尔多鳍鱼）的HoxA基因簇进行了测序和分析，多鳍鱼是一种系统发育基部的辐鳍鱼。独立的证据表明，多鳍鱼有一个HoxA基因簇，相对于人类和鲨鱼的HoxA基因簇，以及斑马鱼、河豚和条纹鲈的HoxAα和HoxAβ基因簇，其非编码序列保守模式和基因保留模式是镶嵌的。多鳍鱼和真骨鱼类之间保守的HoxA基因簇非编码序列表明，新的顺式序列是在辐鳍鱼干群中获得的，并在基因簇重复后得以保留。因此，在最早的辐鳍鱼中，单个HoxA基因簇的进化已经比人类和鲨鱼中的更具动态性。这种趋势在硬骨鱼的HoxA基因簇重复后达到顶峰。
