Systematic variation in the pattern of gene paralog retention between the teleost superorders ostariophysi and acanthopterygii

Genome Biology and Evolution

Volumn 6, Issue 4, 2014, Pages 981-987

  De La Serrana, Daniel Garcia ^a   Mareco, Edson A ^b   Johnston, Ian A ^a  

^a UNIVERSITY OF ST ANDREWS   (United Kingdom)

^b SÃO PAULO STATE UNIVERSITY UNESP   (Brazil)

Author keywords

Fish evolution; Gene loss; Ploidy; Whole genome duplication

Indexed keywords

ANIMAL; FISH; GENE DUPLICATION; GENETICS; GENOME; HUMAN; MOLECULAR EVOLUTION; PHYSIOLOGY;

ANIMALS; EVOLUTION, MOLECULAR; FISHES; GENE DUPLICATION; GENOME; HUMANS;

EID: 84902951850     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evu074     Document Type: Article

References (30)

1. Bowers JE, Chapman BA, Rong J, Paterson AH. 2003. Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 422:433-438.
2. Braasch I, Postlethwaite J. 2012. Fish polyploidy and the teleost genome duplication. In: Soltis PS, Soltis DE, editors. Polyploidy and genome evolution. Berlin (Germany): Springer. p. 341-383.
3. Brunet FG, et al. 2006. Gene loss and evolutionary rates following wholegenome duplication in teleost fish. Mol Biol Evol. 23:1808-1816.
4. Dehal P, Boore JL. 2005. Two rounds of whole genome duplication in the ancestral vertebrate. PLoS Biol. 3(10):e14.
5. Dereeper A, et al. 2008. Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Res. 36:465-469.
6. Drummond AJ, Suchard MA, Xie D, Rambaut A. 2012. Bayesian phylogenetics with the BEAUti and the BEAST 1.7. Mol Biol Evol. 29: 1969-1973.
7. Franceschini A, et al. 2013. STRING v91.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res. 41: 808-815.
8. Garcia de la Serrana D, Estevez A, Andree K, Johnston IA. 2012. Fast skeletal muscle transcriptome of the Gilthead sea bream (Sparus aurata) determined by next generation sequencing. BMC Genomics 13:181.
9. Jaillon O, et al. 2004. Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature 431: 946-957.
10. Jiao Y, et al. 2011. Ancestral polyploidy in seed plants and angiosperms. Nature 473:97-100.
11. Johnston IA, Bower NI,Macqueen DJ. 2011. Growth and the regulation of myotomal muscle mass in teleost fish. J Exp Biol. 214:1617-1628.
12. Kasahara M, et al. 2007. The medaka draft genome and insights into vertebrate genome evolution. Nature 447:714-719.
13. Kumar JP. 2009. The sine oculis homoeobox (SIX) family of transcription factors as regulators of development and disease. Cell Mol Life Sci. 66: 565-583.
14. Kuraku S, Meyer A. 2009. The evolution and maintenance of Hox gene clusters in vertebrates and the teleost-specific genome duplication. Int J Dev Biol. 53:765-774.
15. Louis A, Muffato M, Roest CH. 2013. Genomicus: five genome browsers for comparative genomics in eukaryotes. Nucleic Acids Res. 41(Database issue):D700-D705.
16. Mable BK, Alexandrou MA, Taylor MI. 2011. Genome duplication in amphibians and fish: an extended synthesis. J Zool. 284:151-182.
17. Macqueen DJ, Johnston IA. 2014. A well-constrained estimate for the timing of the salmonid whole genome duplication reveals major decoupling from species diversification. Proc Roy Soc B. 281: 20132881.
18. Maere S, Van de Peer Y. 2010. Duplicate retention after small and largescale duplications. In: Dittmar K, Liberles D, editors. Evolution after gene duplication. Chapter 3. Hoboken (NJ):Wiley-Blackwell. p. 31-56.
19. Mallo M, Wellik DM, Deschamps J. 2010. Hox genes and regional patterning of the vertebrate body plan. Dev Biol. 344:7-15.
20. McCormick F. 1995. Ras-related proteins in signal transduction and growth control. Mol Reprod Dev. 42:500-506.
21. Nelson JS. 2006. Fishes of the world. Hoboken (NJ): Wiley-Blackwell.
22. Penn O, et al. 2010. Guidance: A web server for assessing alignment confidence scores. Nucleic Acids Res. 38:23-28.
23. Santini F, Harmon LJ, Carnevale G, Alfaro ME. 2009. Did genome duplication drive the origin of teleosts? A comparative study of diversification in ray-finned fishes. BMC Evol Biol. 9:194.
24. Sarkar A, Hochedlinger K. 2013. The sox family of transcription factors: Versatile regulators of stem and progenitor cell fate. Cell Stem Cell. 12: 15-30.
25. Sato Y, Nishida M. 2010. Teleost fish with specific genome duplication as unique models of vertebrate evolution. Environ Biol Fish. 88:169-188.
26. Steinke D, Salzburger W, Meyer A. 2006. Novel relationships among ten fish model species revealed based on phylogenomic analysis using ESTs. J Mol Evol. 62:722-784.
27. Taylor JS, Braasch I, Frickey T, Meyer A, Van de Peer Y. 2003. Genome duplications, a trait shared by 2200 species of ray-finned fish. Genome Res. 13:382-390.
28. Taylor JS, Van de Peer Y, Meyer A. 2001. Genome duplication, divergent resolution and speciation. Trends Genet. 17(6):299-301.
29. Tamura K, et al. 2010. MEGA5: molecular evolutionary genetic analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 28:2731-2739.
30. Zhan SH, Glick L, Tsigenopoulos CS, Otto SP, Mayrose I. 2014. Comparative analysis reveals that polyploidy does not accelerate diversification in fish. J Evol Biol. 27:391-403.