title: The fate of recent duplicated genes following a fourth-round whole genome duplication in a tetraploid fish, common carp (Cyprinus carpio).
abstract: Whole genome duplication (WGD) results in extensive genetic redundancy. In plants and yeast, WGD is followed by rapid gene deletions and intense expression differentiation with slow functional divergence. However, the early evolution of the gene differentiation processes is poorly understood in vertebrates because almost all studied WGDs are extremely ancient, and the genomes have returned to a diploid status. Common carp had a very recent fourth round of WGD dated to 8 million years ago. It therefore constitutes an ideal model to study early-stage functional divergence and expression differentiation in vertebrates. We identified 1,757 pairs of recently duplicated genes (RDGs) originating from this specific WGD and found that most ancestral genes were retained in duplicate. Most RDGs were conserved and under selective pressure. Gene expression analysis across six tissues revealed that 92.5% of RDG pairs were co-expressed in at least one tissue and that the expression of nearly half pairs ceased to be strongly correlated, indicating slow spatial divergence but rapid expression dissociation. Functional comparison revealed that 25% of pairs had functional divergence, of which neo- and sub-functionalization were the main outcomes. Our analysis revealed slow gene loss but rapid and intense expression and function differentiation after WGD.
authors: CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, 100141, China.
authors: Jiong-Tang
authors: JT
authors: Li
authors: CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, 100141, China.
authors: Guang-Yuan
authors: GY
authors: Hou
authors: 1] CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, 100141, China [2] College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China.
authors: Xiang-Fei
authors: XF
authors: Kong
authors: 1] CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, 100141, China [2] College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China [3] Tianjin Fisheries Research Institute, Tianjin, 300221, China.
authors: Chun-Yan
authors: CY
authors: Li
authors: CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, 100141, China.
authors: Jian-Ming
authors: JM
authors: Zeng
authors: CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, 100141, China.
authors: Heng-De
authors: HD
authors: Li
authors: 1] CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, 100141, China [2] College of Life Science and Technology, Dalian Ocean University, Dalian, 116023, China.
authors: Gui-Bao
authors: GB
authors: Xiao
authors: 1] CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, 100141, China [2] College of Life Science and Technology, Dalian Ocean University, Dalian, 116023, China.
authors: Xiao-Min
authors: XM
authors: Li
authors: CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, 100141, China.
authors: Xiao-Wen
authors: XW
authors: Sun
mesh_terms: D000818:Animals; D005075:Biological Evolution; D002347:Carps / Q000235:genetics*; D030541:Databases, Genetic; D020440:Gene Duplication; D016678:Genome; D017423:Sequence Analysis, RNA; D015027:Zebrafish / Q000235:genetics
references: Genetics. 1999 Apr;151(4):1531-45
references: 10101175
references: Nat Biotechnol. 2012 Jan;30(1):99-104
references: 22081020
references: Genetics. 2006 Jan;172(1):507-17
references: 16172500
references: Mol Biol Evol. 2003 Sep;20(9):1425-34
references: 12832638
references: Nat Rev Genet. 2001 May;2(5):333-41
references: 11331899
references: Nature. 1997 Jun 12;387(6634):708-13
references: 9192896
references: Genome Res. 2002 Apr;12(4):656-64
references: 11932250
references: Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W116-20
references: 15980438
references: BMC Genomics. 2013;14:778
references: 24215113
references: Mol Phylogenet Evol. 1994 Mar;3(1):59-68
references: 8025730
references: DNA Res. 2011 Aug;18(4):253-61
references: 21676972
references: Mol Biol Evol. 2006 Sep;23(9):1808-16
references: 16809621
references: Bioinformatics. 2009 May 1;25(9):1105-11
references: 19289445
references: Nature. 2007 Jun 7;447(7145):714-9
references: 17554307
references: Nat Genet. 2014 Nov;46(11):1212-9
references: 25240282
references: Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W293-7
references: 16845012
references: Mol Biol Evol. 2007 Aug;24(8):1586-91
references: 17483113
references: Proc Natl Acad Sci U S A. 2007 Dec 4;104(49):19428-33
references: 18040051
references: Nature. 2004 Apr 8;428(6983):617-24
references: 15004568
references: BMC Evol Biol. 2005;5:28
references: 15831095
references: J Hered. 2007 Mar-Apr;98(2):136-41
references: 17208934
references: BMC Genomics. 2012;13:96
references: 22424280
references: Bioinformatics. 2005 Sep 15;21(18):3674-6
references: 16081474
references: Trends Genet. 2000 Jun;16(6):276-7
references: 10827456
references: PLoS Comput Biol. 2014 Mar;10(3):e1003517
references: 24651478
references: Genome Res. 2004 Oct;14(10A):1870-9
references: 15466287
references: Nat Rev Genet. 2010 Feb;11(2):97-108
references: 20051986
references: Plant J. 2013 Jan;73(1):143-53
references: 22974547
references: Trends Genet. 2002 Dec;18(12):609-13
references: 12446139
references: Bioinformatics. 2010 Jan 1;26(1):136-8
references: 19855105
references: Nature. 2013 Apr 25;496(7446):498-503
references: 23594743
references: Zebrafish. 2012 Jun;9(2):59-67
references: 22715948
references: Genome Res. 2003 Jan;13(1):108-17
references: 12529313
references: Genome Res. 2003 Jul;13(7):1638-45
references: 12840042
references: Trends Genet. 2005 Nov;21(11):602-7
references: 16140417
references: Nat Protoc. 2012 Mar;7(3):562-78
references: 22383036
references: Genome Res. 2000 Apr;10(4):516-22
references: 10779491
references: Int J Plant Genomics. 2008;2008:619832
references: 18483572
references: Gene. 1995 Feb 14;153(2):231-6
references: 7875594
references: PLoS One. 2012;7(10):e48140
references: 23110192
references: Genetics. 2004 Feb;166(2):935-45
references: 15020478
references: Proc Natl Acad Sci U S A. 2008 Jun 17;105(24):8333-8
references: 18541921
references: Nucleic Acids Res. 2002 Jan 1;30(1):38-41
references: 11752248
references: Curr Opin Genet Dev. 2009 Dec;19(6):600-6
references: 19900800
references: Curr Opin Genet Dev. 1996 Dec;6(6):715-22
references: 8994842