Gene Duplication in an African Cichlid Adaptive Radiation

Overview

Journal BMC Genomics

Publisher Biomed Central

Specialty Genetics

Date 2014 Feb 28

PMID 24571567

Citations 7

Authors

Heather E Machado

Ginger Jui

Domino A Joyce

Christian R L Reilly 3rd

David H Lunt

Suzy C P Renn

Affiliations

Soon will be listed here.

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.

Citing Articles

Correspondence of aCGH and long-read genome assembly for detection of copy number differences: A proof-of-concept with cichlid genomes.

Preising G, Faber-Hammond J, Renn S PLoS One. 2021; 16(10):e0258193.

PMID: 34618847 PMC: 8496808. DOI: 10.1371/journal.pone.0258193.

Evolutionary Analysis of OAT Gene Family in River and Swamp Buffalo: Potential Role of Gene in Milk Performance.

Ma X, Liang S, Liang A, Rushdi H, Deng T Genes (Basel). 2021; 12(9).

PMID: 34573376 PMC: 8472334. DOI: 10.3390/genes12091394.

Insights into the Function and Evolution of Taste 1 Receptor Gene Family in the Carnivore Fish Gilthead Seabream ().

Angotzi A, Puchol S, Cerda-Reverter J, Morais S Int J Mol Sci. 2020; 21(20).

PMID: 33086689 PMC: 7594079. DOI: 10.3390/ijms21207732.

The Genomic Substrate for Adaptive Radiation: Copy Number Variation across 12 Tribes of African Cichlid Species.

Faber-Hammond J, Bezault E, Lunt D, Joyce D, Renn S Genome Biol Evol. 2019; 11(10):2856-2874.

PMID: 31504491 PMC: 6795240. DOI: 10.1093/gbe/evz185.

Madagascar ground gecko genome analysis characterizes asymmetric fates of duplicated genes.

Hara Y, Takeuchi M, Kageyama Y, Tatsumi K, Hibi M, Kiyonari H BMC Biol. 2018; 16(1):40.

PMID: 29661185 PMC: 5901865. DOI: 10.1186/s12915-018-0509-4.

References

Liu T, Bhuiyan S, Snow R, Yasuda S, Yasuda T, Yang Y . Identification and characterization of two novel cytosolic sulfotransferases, SULT1 ST7 and SULT1 ST8, from zebrafish. Aquat Toxicol. 2008; 89(2):94-102. DOI: 10.1016/j.aquatox.2008.06.005. View

Barreiro L, Quintana-Murci L . From evolutionary genetics to human immunology: how selection shapes host defence genes. Nat Rev Genet. 2009; 11(1):17-30. DOI: 10.1038/nrg2698. View

Persson A, Stet R, Pilstrom L . Characterization of MHC class I and beta(2)-microglobulin sequences in Atlantic cod reveals an unusually high number of expressed class I genes. Immunogenetics. 1999; 50(1-2):49-59. DOI: 10.1007/s002510050685. View

Fischer H, Wheat C, Heckel D, Vogel H . Evolutionary origins of a novel host plant detoxification gene in butterflies. Mol Biol Evol. 2008; 25(5):809-20. DOI: 10.1093/molbev/msn014. View

Loh Y, Katz L, Mims M, Kocher T, Yi S, Streelman J . Comparative analysis reveals signatures of differentiation amid genomic polymorphism in Lake Malawi cichlids. Genome Biol. 2008; 9(7):R113. PMC: 2530870. DOI: 10.1186/gb-2008-9-7-r113. View

Tanaka H, Ishibashi J, Fujita K, Nakajima Y, Sagisaka A, Tomimoto K . A genome-wide analysis of genes and gene families involved in innate immunity of Bombyx mori. Insect Biochem Mol Biol. 2008; 38(12):1087-110. DOI: 10.1016/j.ibmb.2008.09.001. View

Fortna A, Kim Y, MacLaren E, Marshall K, Hahn G, Meltesen L . Lineage-specific gene duplication and loss in human and great ape evolution. PLoS Biol. 2004; 2(7):E207. PMC: 449870. DOI: 10.1371/journal.pbio.0020207. View

Fujimura K, Conte M, Kocher T . Circular DNA intermediate in the duplication of Nile tilapia vasa genes. PLoS One. 2012; 6(12):e29477. PMC: 3245284. DOI: 10.1371/journal.pone.0029477. View

Miller K, Withler R . The salmonid class I MHC: limited diversity in a primitive teleost. Immunol Rev. 1999; 166:279-93. DOI: 10.1111/j.1600-065x.1998.tb01269.x. View

10.

Renz A, Gunter H, Fischer J, Qiu H, Meyer A, Kuraku S . Ancestral and derived attributes of the dlx gene repertoire, cluster structure and expression patterns in an African cichlid fish. Evodevo. 2011; 2(1):1. PMC: 3024246. DOI: 10.1186/2041-9139-2-1. View

11.

Li W, Gu Z, Wang H, Nekrutenko A . Evolutionary analyses of the human genome. Nature. 2001; 409(6822):847-9. DOI: 10.1038/35057039. View

12.

Fraser G, Hulsey C, Bloomquist R, Uyesugi K, Manley N, Streelman J . An ancient gene network is co-opted for teeth on old and new jaws. PLoS Biol. 2009; 7(2):e31. PMC: 2637924. DOI: 10.1371/journal.pbio.1000031. View

13.

Lie K, Lanzen A, Breilid H, Olsvik P . Gene expression profiling in Atlantic cod (Gadus morhua L.) from two contaminated sites using a custom-made cDNA microarray. Environ Toxicol Chem. 2009; 28(8):1711-21. DOI: 10.1897/08-517.1. View

14.

Machado H, Renn S . A critical assessment of cross-species detection of gene duplicates using comparative genomic hybridization. BMC Genomics. 2010; 11:304. PMC: 2876127. DOI: 10.1186/1471-2164-11-304. View

15.

Farias I, Orti G, Meyer A . Total evidence: molecules, morphology, and the phylogenetics of cichlid fishes. J Exp Zool. 2000; 288(1):76-92. View

16.

van Hijum S, Baerends R, Zomer A, Karsens H, Martin-Requena V, Trelles O . Supervised Lowess normalization of comparative genome hybridization data--application to lactococcal strain comparisons. BMC Bioinformatics. 2008; 9:93. PMC: 2275246. DOI: 10.1186/1471-2105-9-93. View

17.

Van der Aa L, Levraud J, Yahmi M, Lauret E, Briolat V, Herbomel P . A large new subset of TRIM genes highly diversified by duplication and positive selection in teleost fish. BMC Biol. 2009; 7:7. PMC: 2657112. DOI: 10.1186/1741-7007-7-7. View

18.

Sackton T, Lazzaro B, Schlenke T, Evans J, Hultmark D, Clark A . Dynamic evolution of the innate immune system in Drosophila. Nat Genet. 2007; 39(12):1461-8. DOI: 10.1038/ng.2007.60. View

19.

Clop A, Vidal O, Amills M . Copy number variation in the genomes of domestic animals. Anim Genet. 2012; 43(5):503-17. DOI: 10.1111/j.1365-2052.2012.02317.x. View

20.

Lynch M, Conery J . The evolutionary fate and consequences of duplicate genes. Science. 2000; 290(5494):1151-5. DOI: 10.1126/science.290.5494.1151. View