title: Twisted signatures of GC-biased gene conversion embedded in an evolutionary stable karyotype.
abstract: The genomes of many vertebrates show a characteristic heterogeneous distribution of GC content, the so-called GC isochore structure. The origin of isochores has been explained via the mechanism of GC-biased gene conversion (gBGC). However, although the isochore structure is declining in many mammalian genomes, the heterogeneity in GC content is being reinforced in the avian genome. Despite this discrepancy, which remains unexplained, examinations of individual substitution frequencies in mammals and birds are both consistent with the gBGC model of isochore evolution. On the other hand, a negative correlation between substitution and recombination rate found in the chicken genome is inconsistent with the gBGC model. It should therefore be important to consider along with gBGC other consequences of recombination on the origin and fate of mutations, as well as to account for relationships between recombination rate and other genomic features. We therefore developed an analytical model to describe the substitution patterns found in the chicken genome, and further investigated the relationships between substitution patterns and several genomic features in a rigorous statistical framework. Our analysis indicates that GC content itself, either directly or indirectly via interrelations to other genomic features, has an impact on the substitution pattern. Further, we suggest that this phenomenon is particularly visible in avian genomes due to their unusually low rate of chromosomal evolution. Because of this, interrelations between GC content and other genomic features are being reinforced, and are as such more pronounced in avian genomes as compared with other vertebrate genomes with a less stable karyotype.
authors.affiliation: Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.
authors.forename: Carina F
authors.initials: CF
authors.lastname: Mugal
authors.forename: Peter F
authors.initials: PF
authors.lastname: Arndt
authors.forename: Hans
authors.initials: H
authors.lastname: Ellegren
mesh_terms: D000818:Animals; D001482:Base Composition; D002645:Chickens; D002875:Chromosomes / Q000235:genetics*; D019143:Evolution, Molecular; D005785:Gene Conversion; D016678:Genome; D032085:Isochores / Q000235:genetics; D059785:Karyotype; D008322:Mammals / Q000235:genetics; D011995:Recombination, Genetic; D014714:Vertebrates / Q000235:genetics
chemical_list: D032085:Isochores
keywords: GC isochores; base composition; birds; gene conversion; karyotype; recombination
references.citation: Genetics. 2002 Dec;162(4):1837-47
references.pmid: 12524353
references.citation: PLoS Biol. 2011 Jun;9(6):e1000622
references.pmid: 21697975
references.citation: Nature. 2012 May 13;485(7400):642-5
references.pmid: 22660327
references.citation: Mol Biol Evol. 2004 Jun;21(6):984-90
references.pmid: 14963104
references.citation: BMC Genomics. 2013 Feb 08;14:86
references.pmid: 23394684
references.citation: Gene. 2008 Aug 1;419(1-2):62-5
references.pmid: 18436395
references.citation: Mol Biol Evol. 2005 Mar;22(3):650-8
references.pmid: 15537806
references.citation: Nat Rev Genet. 2007 Dec;8(12):950-62
references.pmid: 18007651
references.citation: Genome Res. 2005 Jan;15(1):120-5
references.pmid: 15590944
references.citation: Gene. 2000 Jan 4;241(1):3-17
references.pmid: 10607893
references.citation: Proc Natl Acad Sci U S A. 2008 Mar 4;105(9):3433-7
references.pmid: 18305168
references.citation: Cytogenet Genome Res. 2007;119(1-2):113-26
references.pmid: 18160790
references.citation: Nature. 1999 Nov 25;402(6760):411-3
references.pmid: 10586880
references.citation: Am J Hum Genet. 2003 Jun;72(6):1527-35
references.pmid: 12740762
references.citation: Adv Hum Genet. 1994;22:47-115
references.pmid: 7762454
references.citation: PLoS Genet. 2008 May 09;4(5):e1000071
references.pmid: 18464896
references.citation: Trends Ecol Evol. 2010 May;25(5):283-91
references.pmid: 20363047
references.citation: PLoS Biol. 2010 Sep 07;8(9):
references.pmid: 20838655
references.citation: Gene. 1991 Apr;100:181-7
references.pmid: 2055469
references.citation: J Mol Evol. 2004 Jun;58(6):653-60
references.pmid: 15461422
references.citation: Cytogenet Genome Res. 2004;106(1):111-9
references.pmid: 15218250
references.citation: Curr Opin Genet Dev. 2003 Dec;13(6):562-8
references.pmid: 14638315
references.citation: Proc Natl Acad Sci U S A. 1983 Oct;80(20):6278-81
references.pmid: 6578508
references.citation: Heredity (Edinb). 2012 Jan;108(1):28-36
references.pmid: 22108627
references.citation: Science. 2012 Apr 13;336(6078):193-8
references.pmid: 22422862
references.citation: Genome Biol Evol. 2011;3:516-27
references.pmid: 21670083
references.citation: Genetics. 2001 Oct;159(2):907-11
references.pmid: 11693127
references.citation: Annu Rev Genomics Hum Genet. 2009;10:285-311
references.pmid: 19630562
references.citation: Nat Genet. 2009 Apr;41(4):393-5
references.pmid: 19287383
references.citation: PLoS Biol. 2008 Oct 7;6(10):e245
references.pmid: 18842067
references.citation: Hum Mol Genet. 2003 Oct 1;12(19):2411-5
references.pmid: 12915446
references.citation: Trends Genet. 2003 Mar;19(3):128-30
references.pmid: 12615004
references.citation: J Mol Biol. 1973 Oct 15;80(1):177-97
references.pmid: 4798988
references.citation: Genetics. 2002 Dec;162(4):1805-10
references.pmid: 12524350
references.citation: Mol Biol Evol. 2006 Jun;23(6):1203-16
references.pmid: 16551647
references.citation: Chromosome Res. 1999;7(4):289-95
references.pmid: 10461874
references.citation: Genome Res. 2005 Jan;15(1):98-110
references.pmid: 15590940
references.citation: PLoS Genet. 2009 Dec;5(12):e1000753
references.pmid: 19997497
references.citation: Genome Res. 2009 Mar;19(3):510-9
references.pmid: 19088305
references.citation: Trends Genet. 2012 Mar;28(3):101-9
references.pmid: 22154475
references.citation: Nat Rev Genet. 2011 Oct 04;12(11):756-66
references.pmid: 21969038
references.citation: BMC Genomics. 2009 Jan 14;10:22
references.pmid: 19144180
references.citation: Gene. 1993 Dec 15;135(1-2):57-66
references.pmid: 8276279
references.citation: Cytogenet Genome Res. 2007;117(1-4):64-77
references.pmid: 17675846
references.citation: Genome Res. 2005 Jan;15(1):111-9
references.pmid: 15590946
references.citation: Genome Res. 2010 Aug;20(8):1001-9
references.pmid: 20530252
references.citation: Cytogenet Genome Res. 2007;116(3):167-72
references.pmid: 17317955
references.citation: Science. 2010 Jul 2;329(5987):82-5
references.pmid: 20595613
references.citation: Heredity (Edinb). 2012 Jan;108(1):37-41
references.pmid: 22045382
references.citation: Nat Rev Genet. 2001 Jul;2(7):549-55
references.pmid: 11433361
references.citation: PLoS Genet. 2007 Aug;3(8):e136
references.pmid: 17708682
references.citation: Genome Biol. 2008 Apr 30;9(4):R76
references.pmid: 18447906
references.citation: Genome Res. 2010 Apr;20(4):485-95
references.pmid: 20357052
references.citation: Nucleic Acids Res. 2003 Sep 1;31(17):5212-20
references.pmid: 12930973
references.citation: BMC Genomics. 2009 Apr 03;10:146
references.pmid: 19344507
references.citation: PLoS Genet. 2012;8(5):e1002680
references.pmid: 22570634