Bichir HoxA Cluster Sequence Reveals Surprising Trends in Ray-Finned Fish Genomic Evolution
Chiu, Chi-hua; Dewar, Ken; Wagner, Gunter 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.
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 HoxA and HoxA 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. Originally published Genome Research, Vol. 14, No. 1, Jan 2004
Chiu, Chi-hua, & Dewar, Ken, & Wagner, Gunter 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.. (January 2004). Bichir HoxA Cluster Sequence Reveals Surprising Trends in Ray-Finned Fish Genomic Evolution. Genome Research, (14:1), p.11-17. Retrieved from http://hdl.handle.net/10342/3243
Chiu, Chi-hua, and Dewar, Ken, and Wagner, Gunter P., and Takahashi, Kazuhiko, and Ruddle, Frank, and Ledje, Christina, and Bartsch, Peter, and Scemama, Jean-Luc, and Stellwag, Edmund, and Fried, Claudia, and Prohaska, Sonja J., and Stadler, Peter F., and Amemiya, Chris T.. "Bichir HoxA Cluster Sequence Reveals Surprising Trends in Ray-Finned Fish Genomic Evolution". Genome Research. 14:1. (11-17.), January 2004. January 28, 2020. http://hdl.handle.net/10342/3243.
Chiu, Chi-hua and Dewar, Ken and Wagner, Gunter P. and Takahashi, Kazuhiko and Ruddle, Frank and Ledje, Christina and Bartsch, Peter and Scemama, Jean-Luc and Stellwag, Edmund and Fried, Claudia and Prohaska, Sonja J. and Stadler, Peter F. and Amemiya, Chris T., "Bichir HoxA Cluster Sequence Reveals Surprising Trends in Ray-Finned Fish Genomic Evolution," Genome Research 14, no. 1 (January 2004), http://hdl.handle.net/10342/3243 (accessed January 28, 2020).
Chiu, Chi-hua, Dewar, Ken, Wagner, Gunter 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.. Bichir HoxA Cluster Sequence Reveals Surprising Trends in Ray-Finned Fish Genomic Evolution. Genome Research. January 2004; 14(1) 11-17. http://hdl.handle.net/10342/3243. Accessed January 28, 2020.
East Carolina University