title: Inferring the history of interchromosomal gene transposition in Drosophila using n-dimensional parsimony.
abstract: Gene transposition puts a new gene copy in a novel genomic environment. Moreover, genes moving between the autosomes and the X chromosome experience change in several evolutionary parameters. Previous studies of gene transposition have not utilized the phylogenetic framework that becomes possible with the availability of whole genomes from multiple species. Here we used parsimonious reconstruction on the genomic distribution of gene families to analyze interchromosomal gene transposition in Drosophila. We identified 782 genes that have moved chromosomes within the phylogeny of 10 Drosophila species, including 87 gene families with multiple independent movements on different branches of the phylogeny. Using this large catalog of transposed genes, we detected accelerated sequence evolution in duplicated genes that transposed when compared to the parental copy at the original locus. We also observed a more refined picture of the biased movement of genes from the X chromosome to the autosomes. The bias of X-to-autosome movement was significantly stronger for RNA-based movements than for DNA-based movements, and among DNA-based movements there was an excess of genes moving onto the X chromosome as well. Genes involved in female-specific functions moved onto the X chromosome while genes with male-specific functions moved off the X. There was a significant overrepresentation of proteins involving chromosomal function among transposed genes, suggesting that genetic conflict between sexes and among chromosomes may be a driving force behind gene transposition in Drosophila.
authors.affiliation: Department of Biology and School of Informatics and Computing, Indiana University, Bloomington, Indiana 47405, USA. mira.han@nescent.org
authors.forename: Mira V
authors.initials: MV
authors.lastname: Han
authors.forename: Matthew W
authors.initials: MW
authors.lastname: Hahn
mesh_terms: D000818:Animals; D020090:Chromosome Segregation; D059006:Chromosomes, Insect; D004251:DNA Transposable Elements; D004330:Drosophila / Q000235:genetics*; D005260:Female; D020440:Gene Duplication; D017344:Genes, Insect; D049750:Genome, Insect; D008297:Male; D011995:Recombination, Genetic
chemical_list: D004251:DNA Transposable Elements
references.citation: Proc Natl Acad Sci U S A. 2006 Feb 28;103(9):3220-5
references.pmid: 16492757
references.citation: PLoS Genet. 2007 Nov;3(11):e197
references.pmid: 17997610
references.citation: Science. 2006 Sep 8;313(5792):1448-50
references.pmid: 16960009
references.citation: Mol Biol Evol. 2006 Nov;23(11):2191-202
references.pmid: 16916943
references.citation: Genetics. 2009 Jan;181(1):177-85
references.pmid: 18984573
references.citation: Genetics. 2004 Apr;166(4):1995-9
references.pmid: 15126414
references.citation: Mol Biol Evol. 1998 May;15(5):568-73
references.pmid: 9580986
references.citation: Genome Res. 2007 Dec;17(12):1880-7
references.pmid: 17989252
references.citation: Mol Biol Evol. 2010 Aug;27(8):1963-78
references.pmid: 20351054
references.citation: Genetics. 2010 May;185(1):95-103
references.pmid: 20215470
references.citation: Evolution. 2003 Jun;57(6):1325-35
references.pmid: 12894940
references.citation: Genome Biol Evol. 2009 Jul 07;1:176-88
references.pmid: 20333188
references.citation: Gene. 2006 Dec 30;385:96-102
references.pmid: 17101240
references.citation: Proc Natl Acad Sci U S A. 1983 Jul;80(13):4079-83
references.pmid: 6575397
references.citation: Evolution. 1984 Jul;38(4):735-742
references.pmid: 28555827
references.citation: Genetics. 2010 Apr;184(4):1067-76
references.pmid: 20065068
references.citation: Nat Genet. 2007 Nov;39(11):1361-8
references.pmid: 17922013
references.citation: BMC Bioinformatics. 2009 Feb 03;10:48
references.pmid: 19192299
references.citation: Nat Protoc. 2009;4(1):44-57
references.pmid: 19131956
references.citation: Cell. 1980 Feb;19(2):365-78
references.pmid: 6244106
references.citation: Cell. 1980 Dec;22(3):845-54
references.pmid: 6780200
references.citation: Mol Biol Evol. 2007 Mar;24(3):679-86
references.pmid: 17179139
references.citation: Science. 2004 Jan 23;303(5657):537-40
references.pmid: 14739461
references.citation: Chromosoma. 1975 Aug 11;51(4):347-56
references.pmid: 1175453
references.citation: Genome Res. 2009 May;19(5):859-67
references.pmid: 19411603
references.citation: Nature. 2007 Nov 8;450(7167):203-18
references.pmid: 17994087
references.citation: J Comput Biol. 2006 Mar;13(2):320-35
references.pmid: 16597243
references.citation: Mol Gen Genet. 1997 Jun;255(1):115-24
references.pmid: 9230904
references.citation: Genetics. 2011 Mar;187(3):919-37
references.pmid: 21220356
references.citation: Genome Res. 2010 Nov;20(11):1526-33
references.pmid: 20798392
references.citation: Evolution. 2004 Feb;58(2):437-40
references.pmid: 15068360
references.citation: Curr Biol. 2010 Aug 24;20(16):1476-81
references.pmid: 20705467
references.citation: Trends Ecol Evol. 2011 May;26(5):222-8
references.pmid: 21397976
references.citation: PLoS Biol. 2008 Apr 1;6(4):e80
references.pmid: 18384235
references.citation: Genome Biol. 2007;8(10):R230
references.pmid: 17971225
references.citation: Nucleic Acids Res. 2002 Apr 1;30(7):1575-84
references.pmid: 11917018
references.citation: Nature. 2007 Nov 8;450(7167):238-41
references.pmid: 17994090
references.citation: Trends Ecol Evol. 2010 Apr;25(4):215-23
references.pmid: 19931208
references.citation: Pac Symp Biocomput. 2009;:114-25
references.pmid: 19213133
references.citation: Genetics. 2008 Jul;179(3):1601-55
references.pmid: 18622037
references.citation: Evolution. 2010 Jun;64(6):1541-57
references.pmid: 20298429
references.citation: Genome Res. 2009 May;19(5):897-903
references.pmid: 19251740
references.citation: Genome Biol. 2007;8(1):R11
references.pmid: 17233920
references.citation: Genome Res. 2002 Dec;12(12):1854-9
references.pmid: 12466289
references.citation: Genome Res. 2011 Dec;21(12):2087-95
references.pmid: 22135405
references.citation: Nucleic Acids Res. 2005 Jan 20;33(2):511-8
references.pmid: 15661851
references.citation: Trends Genet. 2003 May;19(5):243-7
references.pmid: 12711214