title: A critical assessment of cross-species detection of gene duplicates using comparative genomic hybridization.
abstract: BACKGROUND
  Comparison of genomic DNA among closely related strains or species is a powerful approach for identifying variation in evolutionary processes. One potent source of genomic variation is gene duplication, which is prevalent among individuals and species. Array comparative genomic hybridization (aCGH) has been successfully utilized to detect this variation among lineages. Here, beyond the demonstration that gene duplicates among species can be quantified with aCGH, we consider the effect of sequence divergence on the ability to detect gene duplicates.
  
  
  RESULTS
  Using the X chromosome genomic content difference between male D. melanogaster and female D. yakuba and D. simulans, we describe a decrease in the ability to accurately measure genomic content (copy number) for orthologs that are only 90% identical. We demonstrate that genome characteristics (e.g. chromatin environment and non-orthologous sequence similarity) can also affect the ability to accurately measure genomic content. We describe a normalization strategy and statistical criteria to be used for the identification of gene duplicates among any species group for which an array platform is available from a closely related species.
  
  
  CONCLUSIONS
  Array CGH can be used to effectively identify gene duplication and genome content; however, certain biases are present due to sequence divergence and other genome characteristics resulting from the divergence between lineages. Highly conserved gene duplicates will be more readily recovered by aCGH. Duplicates that have been retained for a selective advantage due to directional selection acting on many loci in one or both gene copies are likely to be under-represented. The results of this study should inform the interpretation of both previously published and future work that employs this powerful technique.
authors.affiliation: Department of Biology, Reed College, Portland, OR 97202, USA.
authors.forename: Heather E
authors.initials: HE
authors.lastname: Machado
authors.forename: Suzy C P
authors.initials: SC
authors.lastname: Renn
mesh_terms: D000818:Animals; D055028:Comparative Genomic Hybridization; D004330:Drosophila / Q000145:classification / Q000235:genetics*; D005260:Female; D020131:Genes, Duplicate; D008297:Male; D014960:X Chromosome
references.citation: Curr Opin Plant Biol. 2005 Apr;8(2):122-8
references.pmid: 15752990
references.citation: Science. 2000 Nov 10;290(5494):1151-5
references.pmid: 11073452
references.citation: Proc Natl Acad Sci U S A. 2008 Jul 8;105(27):9272-7
references.pmid: 18583475
references.citation: Microbiol Immunol. 2004;48(4):263-9
references.pmid: 15107536
references.citation: BMC Genomics. 2009 Aug 26;10:401
references.pmid: 19709427
references.citation: Genome Res. 2007 Sep;17(9):1266-77
references.pmid: 17666543
references.citation: BMC Genomics. 2005 Nov 10;6:158
references.pmid: 16283928
references.citation: Genomics. 2005 Jun;85(6):790-3
references.pmid: 15885505
references.citation: PLoS Biol. 2005 Sep;3(9):e285
references.pmid: 16076241
references.citation: PLoS Genet. 2007 Nov;3(11):e197
references.pmid: 17997610
references.citation: Science. 2002 Sep 27;297(5590):2253-6
references.pmid: 12351787
references.citation: Nat Genet. 2007 Oct;39(10):1256-60
references.pmid: 17828263
references.citation: Proc Natl Acad Sci U S A. 2007 Dec 11;104(50):19920-5
references.pmid: 18056801
references.citation: Science. 2002 Aug 9;297(5583):1003-7
references.pmid: 12169732
references.citation: Curr Opin Plant Biol. 2005 Apr;8(2):135-41
references.pmid: 15752992
references.citation: Science. 2006 Apr 28;312(5773):577-9
references.pmid: 16645095
references.citation: Genome Res. 2001 Apr;11(4):547-54
references.pmid: 11282970
references.citation: Mol Biol Evol. 2007 Apr;24(4):1056-67
references.pmid: 17283366
references.citation: J Bacteriol. 2009 Jun;191(12):3881-91
references.pmid: 19376880
references.citation: Genome Res. 2003 Mar;13(3):347-57
references.pmid: 12618365
references.citation: Nat Rev Genet. 2006 Feb;7(2):85-97
references.pmid: 16418744
references.citation: Biotechniques. 2000 Sep;29(3):548-50, 552-4, 556  passim
references.pmid: 10997270
references.citation: PLoS Biol. 2004 Jul;2(7):E207
references.pmid: 15252450
references.citation: Genome Res. 2009 Sep;19(9):1586-92
references.pmid: 19657104
references.citation: J Mol Evol. 2007 Nov;65(5):574-88
references.pmid: 17957399
references.citation: Genome Res. 2003 Sep;13(9):2018-29
references.pmid: 12952873
references.citation: Genome Res. 2006 Jun;16(6):787-95
references.pmid: 16702412
references.citation: Genetics. 1999 Apr;151(4):1531-45
references.pmid: 10101175
references.citation: BMC Bioinformatics. 2004 May 05;5:54
references.pmid: 15128431
references.citation: Annu Rev Genet. 2004;38:615-43
references.pmid: 15568988
references.citation: J Mol Evol. 1999 May;48(5):555-64
references.pmid: 10198121
references.citation: Genome Biol. 2008 Apr 22;9(4):R75
references.pmid: 18430225
references.citation: Annu Rev Genomics Hum Genet. 2005;6:331-54
references.pmid: 16124865
references.citation: Trends Genet. 2007 Apr;23(4):200-7
references.pmid: 17313995
references.citation: EMBO J. 1996 Apr 1;15(7):1715-25
references.pmid: 8612596
references.citation: Genome Res. 2004 May;14(5):789-801
references.pmid: 15123579
references.citation: Proc Natl Acad Sci U S A. 2001 Aug 14;98(17):9853-8
references.pmid: 11493693
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: Mol Biol Evol. 2002 Jun;19(6):918-25
references.pmid: 12032248
references.citation: BMC Genomics. 2005 May 27;6:78
references.pmid: 15918914
references.citation: Mol Biol Evol. 2006 Dec;23(12):2467-73
references.pmid: 16980576
references.citation: Genome Biol. 2006;7(5):R43
references.pmid: 16723033
references.citation: PLoS Genet. 2008 Dec;4(12):e1000305
references.pmid: 19079581
references.citation: Proc Natl Acad Sci U S A. 2002 Oct 1;99(20):12963-8
references.pmid: 12297621
references.citation: Trends Genet. 2002 Jan;18(1):29-34
references.pmid: 11750698
references.citation: Appl Environ Microbiol. 2001 Apr;67(4):1911-21
references.pmid: 11282649
references.citation: Nat Genet. 1998 Oct;20(2):207-11
references.pmid: 9771718
references.citation: Genome Res. 2001 May;11(5):653-6
references.pmid: 11337463
references.citation: Genome Biol. 2004;5(6):R42
references.pmid: 15186493
references.citation: Proc Natl Acad Sci U S A. 2004 Aug 17;101(33):12232-5
references.pmid: 15304653
references.citation: Genome Res. 2004 Oct;14(10A):1870-9
references.pmid: 15466287
references.citation: Nat Genet. 2002 Apr;30(4):411-5
references.pmid: 11925567
references.citation: BMC Bioinformatics. 2005 Nov 18;6:274
references.pmid: 16297240
references.citation: Stat Appl Genet Mol Biol. 2004;3:Article3
references.pmid: 16646809
references.citation: Am Nat. 2000 Dec;156(6):590-605
references.pmid: 29592543
references.citation: Proc Natl Acad Sci U S A. 2008 Sep 2;105(35):12944-9
references.pmid: 18753634
references.citation: BMC Bioinformatics. 2008 Feb 11;9:93
references.pmid: 18267014
references.citation: Genome Res. 2007 Feb;17(2):240-8
references.pmid: 17189378
references.citation: BMC Genomics. 2010 Apr 29;11:271
references.pmid: 20429934
references.citation: Nature. 2009 Feb 12;457(7231):877-81
references.pmid: 19212409
references.citation: Proc Natl Acad Sci U S A. 1998 Mar 31;95(7):3708-13
references.pmid: 9520431
references.citation: BMC Evol Biol. 2008 Sep 05;8:245
references.pmid: 18775065
references.citation: Nature. 2006 Nov 23;444(7118):444-54
references.pmid: 17122850
references.citation: BMC Genomics. 2007 Oct 22;8:382
references.pmid: 17953745
references.citation: Proc Natl Acad Sci U S A. 2002 Feb 5;99(3):1556-61
references.pmid: 11818571