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Gene duplication in an African cichlid adaptive radiation

Joyce, Domino A; Renn, Suzy Cp; Reilly, Christian RL; Machado, Heather E.; Reilly, Christian R.L.; Renn, Suzy C.P.; Renn, Suzy C. P.; Machado, Heather E; Jui, Ginger; Joyce, Domino A.; Reilly, Christian R. L.; Lunt, David H.; Renn, Suzy CP

Authors

Domino A Joyce

Suzy Cp Renn

Christian RL Reilly

Heather E. Machado

Christian R.L. Reilly

Suzy C.P. Renn

Suzy C. P. Renn

Heather E Machado

Ginger Jui

Christian R. L. Reilly

Suzy CP Renn



Abstract

Background Gene duplication is a source of evolutionary innovation and can contribute to the divergence of lineages; however, the relative importance of this process remains to be determined. The explosive divergence of the African cichlid adaptive radiations provides both a model for studying the general role of gene duplication in the divergence of lineages and also an exciting foray into the identification of genomic features that underlie the dramatic phenotypic and ecological diversification in this particular lineage. We present the first genome-wide study of gene duplication in African cichlid fishes, identifying gene duplicates in three species belonging to the Lake Malawi adaptive radiation (Metriaclima estherae, Protomelas similis, Rhamphochromis “chilingali”) and one closely related species from a non-radiated riverine lineage (Astatotilapia tweddlei). Results Using Astatotilapia burtoni as reference, microarray comparative genomic hybridization analysis of 5689 genes reveals 134 duplicated genes among the four cichlid species tested. Between 51 and 55 genes were identified as duplicated in each of the three species from the Lake Malawi radiation, representing a 38%–49% increase in number of duplicated genes relative to the non-radiated lineage (37 genes). Duplicated genes include several that are involved in immune response, ATP metabolism and detoxification. Conclusions These results contribute to our understanding of the abundance and type of gene duplicates present in cichlid fish lineages. The duplicated genes identified in this study provide candidates for the analysis of functional relevance with regard to phenotype and divergence. Comparative sequence analysis of gene duplicates can address the role of positive selection and adaptive evolution by gene duplication, while further study across the phylogenetic range of cichlid radiations (and more generally in other adaptive radiations) will determine whether the patterns of gene duplication seen in this study consistently accompany rapid radiation.

Citation

Machado, H. E., Jui, G., Joyce, D. A., Reilly, C. R. L., Lunt, D. H., & Renn, S. C. (2014). Gene duplication in an African cichlid adaptive radiation. BMC Genomics, 15(1), 161. https://doi.org/10.1186/1471-2164-15-161

Acceptance Date Feb 19, 2014
Publication Date Feb 26, 2014
Deposit Date Mar 22, 2016
Publicly Available Date Mar 22, 2016
Journal BMC genomics
Print ISSN 1471-2164
Electronic ISSN 1471-2164
Publisher Springer Verlag
Peer Reviewed Peer Reviewed
Volume 15
Issue 1
Article Number ARTN 161
Pages 161
DOI https://doi.org/10.1186/1471-2164-15-161
Keywords Cichlids; Gene duplication; Adaptive radiation
Public URL https://hull-repository.worktribe.com/output/433990
Publisher URL http://www.biomedcentral.com/1471-2164/15/161
Copyright Statement © 2014 Machado et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
Additional Information Copy of article first published in: BMC genomics, 2014, v.15, issue 1.

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Copyright Statement
© 2014 Machado et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.



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