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The Circadian Clock of Teleost Fish: A Comparative Analysis Reveals Distinct Fates for Duplicated Genes

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Abstract

The circadian clock is a central oscillator that coordinates endogenous rhythms. Members of six gene families underlie the metabolic machinery of this system. Although this machinery appears to correspond to a highly conserved genetic system in metazoans, it has been recognized that vertebrates possess a more diverse gene inventory than that of non-vertebrates. This difference could have originated in the two successive rounds of whole-genome duplications that took place in the common ancestor of the group. Teleost fish underwent an extra event of whole-genome duplication, which is thought to have provided an abundance of raw genetic material for the biological innovations that facilitated the radiation of the group. In this study, we assessed the relative contributions of whole-genome duplication and small-scale gene duplication to generate the repertoire of genes associated with the circadian clock of teleost fish. To achieve this goal, we annotated genes from six gene families associated with the circadian clock in eight teleost fish species, and we reconstructed their evolutionary history by inferring phylogenetic relationships. Our comparative analysis indicated that teleost species possess a variable repertoire of genes related to the circadian clock gene families and that the actual diversity of these genes has been shaped by a variety of phenomena, such as the complete deletion of ohnologs, the differential retention of genes, and lineage-specific gene duplications. From a functional perspective, the subfunctionalization of two ohnolog genes (PER1a and PER1b) in zebrafish highlights the power of whole-genome duplications to generate biological diversity.

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Acknowledgments

This work was supported by Grants from the Fondo Nacional de Desarrollo Científico y Tecnológico (FONDECYT 1120032) to JCO and from the Programa de Mejoramiento de la Calidad y la Equidad de la Educación Superior (MECESUP AUS1203). JTV holds a MECESUP (AUS0703) doctoral fellowship. JIA holds a CONICYT doctoral fellowship. We also thank Espiritu del Elqui for helpful comments and edits.

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  1. José Ignacio Arroyo

    Present address: Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Alameda 340, Santiago, Chile

Authors and Affiliations

  1. Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile

    Jessica Toloza-Villalobos, José Ignacio Arroyo & Juan C. Opazo

  2. Programa de Doctorado en Ciencias mención Ecología y Evolución, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile

    Jessica Toloza-Villalobos & José Ignacio Arroyo

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  1. Jessica Toloza-Villalobos
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  2. José Ignacio Arroyo
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  3. Juan C. Opazo
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Correspondence to Jessica Toloza-Villalobos or Juan C. Opazo.

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Toloza-Villalobos, J., Arroyo, J.I. & Opazo, J.C. The Circadian Clock of Teleost Fish: A Comparative Analysis Reveals Distinct Fates for Duplicated Genes. J Mol Evol 80, 57–64 (2015). https://doi.org/10.1007/s00239-014-9660-x

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