title: Characterization and inference of gene gain/loss along burkholderia evolutionary history.
abstract: A comparative analysis of 60 complete Burkholderia genomes was conducted to obtain insight in the evolutionary history behind the diversity and pathogenicity at species level. A concatenated multiprotein phyletic pattern and a dataset with Burkholderia clusters of orthologous genes (BuCOGs) were constructed. The extent of horizontal gene transfer (HGT) was assessed using a Markov based probabilistic method. A reconstruction of the gene gains and losses history shows that more than half of the Burkholderia genes families are inferred to have experienced HGT at least once during their evolution. Further analysis revealed that the number of gene gain and loss was correlated with the branch length. Genomic islands (GEIs) analysis based on evolutionary history reconstruction not only revealed that most genes in ancient GEIs were gained but also suggested that the fraction of the genome located in GEIs in the small chromosomes is higher than in the large chromosomes in Burkholderia. The mapping of coexpressed genes onto biological pathway schemes revealed that pathogenicity of Burkholderia strains is probably mainly determined by the gained genes in its ancestor. Taken together, our results strongly support that gene gain and loss especially in ancient evolutionary history play an important role in strain divergence, pathogenicity determinants of Burkholderia and GEIs formation.
authors.affiliation: State Key Laboratory of Rice Biology and Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou 310029, China.
authors.forename: Bo
authors.initials: B
authors.lastname: Zhu
authors.forename: Shengli
authors.initials: S
authors.lastname: Zhou
authors.forename: Miaomiao
authors.initials: M
authors.lastname: Lou
authors.forename: Jun
authors.initials: J
authors.lastname: Zhu
authors.forename: Bin
authors.initials: B
authors.lastname: Li
authors.forename: Guanlin
authors.initials: G
authors.lastname: Xie
authors.forename: Gulei
authors.initials: G
authors.lastname: Jin
authors.forename: René
authors.initials: R
authors.lastname: De Mot
references.citation: PLoS One. 2008 Apr 30;3(4):e2058
references.pmid: 18446194
references.citation: Environ Microbiol. 2003 Sep;5(9):719-29
references.pmid: 12919407
references.citation: Bioinformatics. 2008 Dec 1;24(23):2803-4
references.pmid: 18842600
references.citation: Bioinformatics. 2007 Jan 15;23(2):257-8
references.pmid: 17098774
references.citation: J Bacteriol. 2009 Jan;191(1):261-77
references.pmid: 18931103
references.citation: Philos Trans R Soc Lond B Biol Sci. 2009 Aug 12;364(1527):2229-39
references.pmid: 19571243
references.citation: Bioinformatics. 2007 Jul 1;23(13):i87-96
references.pmid: 17646350
references.citation: FEBS Lett. 1994 Feb 21;339(3):269-75
references.pmid: 8112466
references.citation: FEMS Microbiol Rev. 2009 Mar;33(2):376-93
references.pmid: 19178566
references.citation: FEMS Microbiol Lett. 2007 Jan;266(2):231-5
references.pmid: 17233735
references.citation: Mol Biol Evol. 2010 Mar;27(3):703-13
references.pmid: 19808865
references.citation: Proc Natl Acad Sci U S A. 2004 Sep 28;101(39):14240-5
references.pmid: 15377794
references.citation: FEMS Microbiol Rev. 2009 Nov;33(6):1079-99
references.pmid: 19732156
references.citation: FEMS Microbiol Rev. 2008 Jul;32(4):607-26
references.pmid: 18422616
references.citation: J Bacteriol. 2006 Dec;188(23):8178-88
references.pmid: 16997946
references.citation: Trends Cell Biol. 1999 Dec;9(12):M5-8
references.pmid: 10611671
references.citation: Infect Immun. 2004 Jul;72(7):4172-87
references.pmid: 15213162
references.citation: Mol Biol Evol. 2008 May;25(5):903-11
references.pmid: 18296415
references.citation: Nat Rev Genet. 2003 Feb;4(2):121-32
references.pmid: 12560809
references.citation: Curr Microbiol. 2011 Feb;62(2):650-8
references.pmid: 20882285
references.citation: Nucleic Acids Res. 2004 Jan 1;32(Database issue):D55-8
references.pmid: 14681358
references.citation: Genome Dyn. 2009;6:140-157
references.pmid: 19696499
references.citation: Nat Rev Microbiol. 2005 Feb;3(2):144-56
references.pmid: 15643431
references.citation: Nucleic Acids Res. 2010 Jan;38(Database issue):D408-14
references.pmid: 19843611
references.citation: Mol Ecol. 2010 Jan;19(1):44-52
references.pmid: 20002602
references.citation: Nucleic Acids Res. 2005 Oct 24;33(19):6083-9
references.pmid: 16246909
references.citation: Nucleic Acids Res. 2001 Jan 1;29(1):22-8
references.pmid: 11125040
references.citation: BMC Bioinformatics. 2008 Aug 05;9:329
references.pmid: 18680607
references.citation: PLoS Genet. 2007 Dec;3(12):e231
references.pmid: 18159947
references.citation: Genome Biol. 2004;5(10):R80
references.pmid: 15461798
references.citation: Genome Res. 2003 Sep;13(9):2178-89
references.pmid: 12952885
references.citation: Syst Biol. 2003 Oct;52(5):696-704
references.pmid: 14530136
references.citation: Proc Natl Acad Sci U S A. 2004 Sep 28;101(39):14246-51
references.pmid: 15377793
references.citation: Trends Microbiol. 2006 Jun;14(6):277-86
references.pmid: 16684604
references.citation: Bioinformatics. 2009 Aug 1;25(15):1972-3
references.pmid: 19505945
references.citation: Nature. 2000 May 18;405(6784):299-304
references.pmid: 10830951
references.citation: Nucleic Acids Res. 2004 Mar 19;32(5):1792-7
references.pmid: 15034147
references.citation: Proc Natl Acad Sci U S A. 2006 Oct 17;103(42):15611-6
references.pmid: 17030793
references.citation: BMC Bioinformatics. 2004 Mar 03;5:22
references.pmid: 15113412
references.citation: Proc Natl Acad Sci U S A. 2006 Oct 17;103(42):15280-7
references.pmid: 17030797