Int J Biol Sci 2006; 2(2):66-72. doi:10.7150/ijbs.2.66 This issue

Research Paper

Evolutionary genomics of the recently duplicated amphioxus Hairy genes

Senda Jiménez-Delgado1, Miguel Crespo2, Jon Permanyer1, Jordi Garcia-Fernàndez1 #, Miguel Manzanares2 #

1 Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Avda. Diagonal 645, 08028 Barcelona, Spain
2 Instituto de Investigaciones Biomédicas CSIC-UAM, Arturo Duperier 4, 28029 Madrid, Spain
# Both authors contributed equally to the work

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Jiménez-Delgado S, Crespo M, Permanyer J, Garcia-Fernàndez J, Manzanares M. Evolutionary genomics of the recently duplicated amphioxus Hairy genes. Int J Biol Sci 2006; 2(2):66-72. doi:10.7150/ijbs.2.66. Available from

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Amphioxus Hairy genes have gone through a number of lineage-specific duplications, resulting in eight members, some of which are differentially expressed in the embryo. In order to gain insights into the evolution and function of this gene family we have compared their genomic structure and searched for conserved non-coding sequence elements. We have found that introns have been lost independently from these genes at least twice and after the duplication events. By carrying out phylogenetic footprinting between paralogues expressed in the embryo, we have found a differential distribution of conserved elements that could explain the limited overlap in expression patterns of Hairy genes in the amphioxus embryo. Furthermore, clustering of RBP-Jk binding sites in these conserved elements suggests that amphioxus Hairy genes are downstream targets of the Notch signaling pathway, as occurs in vertebrates. All of this evidence suggests that amphioxus Hairy genes have gone through a process of subfunctionalization shortly after their duplication, representing an extreme and rapid case of the duplication-degeneration-complementation model.

Keywords: amphioxus, DDC model, Hairy, phylogenetic footprinting, evolution