Abstract
There are multiple theories on the evolution of genomic imprinting. We investigated whether the molecular evolution of true orthologs of known imprinted genes provides support for theories based on gene duplication or parental conflicts (where mediated by amino-acid changes). Our analysis of 34 orthologous genes demonstrates that the vast majority of mammalian imprinted genes have not undergone any subsequent significant gene duplication within placental species, suggesting that selection pressures against gene duplication events could be operating for imprinted loci. As antagonistic co-evolution between imprinted genes can regulate offspring growth, proteins mediating this interaction could be subject to rapid evolution via positive selection. Supporting this, we detect evidence of site specific positive selection for the imprinted genes OSBPL5 (and GNASXL), and detect lineage-specific positive selection for 14 imprinted genes where it is known that the gene is imprinted in a specific lineage, namely for: PLAGL1, IGF2, SLC22A18, OSBPL5, DCN, DLK1, RASGRF1, IGF2R, IMPACT, GRB10, NAPIL4, UBE3A, GATM and GABRG3. However, there is an overall lack of concordance between the known imprinting status of each gene (i.e. whether the gene is imprinted or biallelically expressed in a particular mammalian lineage) and positive selection. While only a small number of orthologs of imprinted loci display evidence of positive selection, we observe that the majority of orthologs of imprinted loci display high levels of micro-synteny conservation and have undergone very few cis- or trans-duplications in placental mammalian lineages.
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Acknowledgements
MD & NBL acknowledge funding support from IRCSET. TAW acknowledges funding support from the School of Biotechnology and the Pierse Trust DCU. We would like to thank the Science Foundation Ireland and the Higher Education Authority - Irish Centre for High-End Computing (ICHEC) for processor time and technical support. We are grateful to the comments of two anonymous reviewers on a previous draft of this paper. We would like to thank Dr James McInerney (NUIM, Ireland) and Prof Ken Wolfe (TCD, Ireland) for discussions relating to analysis and for computational facilities. CS and MJOC are funded by Science Foundation Ireland (Grants 08/IN.1/B1931 and EOB2673).
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M.J.O’C, K.J.S and C.S designed research; M.J.O’C, N.B.L, T.A.W. and M.T.A.D. performed research; M.T.A.D, M.J.O’C, N.B.L, T.A.W., and CS prepared Results Figures and Tables, and M.J.O’C and C.S wrote the paper.
Noeleen B. Loughran, Mark T.A. Donoghue contributed equally to this work.
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Supplementary File 6:
Reconciliation of gene and species trees for (a)GATM, (b)COPG2and (c)IMPACT. Gene duplication events for these genes within the imprinted clade are shown as large red circles on the node at which the duplication event/events occurred. The gene duplicate that has been retained is indicated in heavy black lines, while the duplicates that have been lost are shown as pale grey lines. (PDF 203 kb)
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O’Connell, M.J., Loughran, N.B., Walsh, T.A. et al. A phylogenetic approach to test for evidence of parental conflict or gene duplications associated with protein-encoding imprinted orthologous genes in placental mammals. Mamm Genome 21, 486–498 (2010). https://doi.org/10.1007/s00335-010-9283-5
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DOI: https://doi.org/10.1007/s00335-010-9283-5