title: Systematic variation in the pattern of gene paralog retention between the teleost superorders Ostariophysi and Acanthopterygii.
abstract: Teleost fish underwent whole-genome duplication around 450 Ma followed by diploidization and loss of 80-85% of the duplicated genes. To identify a deep signature of this teleost-specific whole-genome duplication (TSGD), we searched for duplicated genes that were systematically and uniquely retained in one or other of the superorders Ostariophysi and Acanthopterygii. TSGD paralogs comprised 17-21% of total gene content. Some 2.6% (510) of TSGD paralogs were present as pairs in the Ostariophysi genomes of Danio rerio (Cypriniformes) and Astyanax mexicanus (Characiformes) but not in species from four orders of Acanthopterygii (Gasterosteiformes, Gasterosteus aculeatus; Tetraodontiformes, Tetraodon nigroviridis; Perciformes, Oreochromis niloticus; and Beloniformes, Oryzias latipes) where a single copy was identified. Similarly, 1.3% (418) of total gene number represented cases where TSGD paralogs pairs were systematically retained in the Acanthopterygian but conserved as a single copy in Ostariophysi genomes. We confirmed the generality of these results by phylogenetic and synteny analysis of 40 randomly selected linage-specific paralogs (LSPs) from each superorder and completed with the transcriptomes of three additional Ostariophysi species (Ictalurus punctatus [Siluriformes], Sinocyclocheilus species [Cypriniformes], and Piaractus mesopotamicus [Characiformes]). No chromosome bias was detected in TSGD paralog retention. Gene ontology (GO) analysis revealed significant enrichment of GO terms relative to the human GO SLIM database for "growth," "Cell differentiation," and "Embryo development" in Ostariophysi and for "Transport," "Signal Transduction," and "Vesicle mediated transport" in Acanthopterygii. The observed patterns of paralog retention are consistent with different diploidization outcomes having contributed to the evolution/diversification of each superorder.
authors.affiliation: School of Biology, Scottish Oceans Institute, University of St Andrews, Fife, United Kingdom.
authors.forename: Daniel
authors.initials: D
authors.lastname: Garcia de la Serrana
authors.forename: Edson A
authors.initials: EA
authors.lastname: Mareco
authors.forename: Ian A
authors.initials: IA
authors.lastname: Johnston
mesh_terms: D000818:Animals; D019143:Evolution, Molecular; D005399:Fishes / Q000235:genetics*; D020440:Gene Duplication / Q000502:physiology*; D016678:Genome / Q000502:physiology*; D006801:Humans
keywords: fish evolution; gene loss; ploidy; whole-genome duplication
references.citation: Nucleic Acids Res. 2013 Jan;41(Database issue):D700-5
references.pmid: 23193262
references.citation: Mol Reprod Dev. 1995 Dec;42(4):500-6
references.pmid: 8607982
references.citation: Nature. 2007 Jun 7;447(7145):714-9
references.pmid: 17554307
references.citation: J Evol Biol. 2014 Feb;27(2):391-403
references.pmid: 24417407
references.citation: Nucleic Acids Res. 2013 Jan;41(Database issue):D808-15
references.pmid: 23203871
references.citation: Nature. 2003 Mar 27;422(6930):433-8
references.pmid: 12660784
references.citation: Mol Biol Evol. 2011 Oct;28(10):2731-9
references.pmid: 21546353
references.citation: BMC Evol Biol. 2009 Aug 08;9:194
references.pmid: 19664233
references.citation: Proc Biol Sci. 2014 Jan 22;281(1778):20132881
references.pmid: 24452024
references.citation: Nature. 2011 May 5;473(7345):97-100
references.pmid: 21478875
references.citation: Cell Stem Cell. 2013 Jan 3;12(1):15-30
references.pmid: 23290134
references.citation: Trends Genet. 2001 Jun;17(6):299-301
references.pmid: 11377777
references.citation: Int J Dev Biol. 2009;53(5-6):765-73
references.pmid: 19557682
references.citation: BMC Genomics. 2012 May 11;13:181
references.pmid: 22577894
references.citation: Genome Res. 2003 Mar;13(3):382-90
references.pmid: 12618368
references.citation: Nucleic Acids Res. 2010 Jul;38(Web Server issue):W23-8
references.pmid: 20497997
references.citation: PLoS Biol. 2005 Oct;3(10):e314
references.pmid: 16128622
references.citation: Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W465-9
references.pmid: 18424797
references.citation: Mol Biol Evol. 2012 Aug;29(8):1969-73
references.pmid: 22367748
references.citation: J Exp Biol. 2011 May 15;214(Pt 10):1617-28
references.pmid: 21525308
references.citation: Nature. 2004 Oct 21;431(7011):946-57
references.pmid: 15496914
references.citation: Dev Biol. 2010 Aug 1;344(1):7-15
references.pmid: 20435029
references.citation: J Mol Evol. 2006 Jun;62(6):772-84
references.pmid: 16752215
references.citation: Mol Biol Evol. 2006 Sep;23(9):1808-16
references.pmid: 16809621
references.citation: Cell Mol Life Sci. 2009 Feb;66(4):565-83
references.pmid: 18989625