Distant horizontal gene transfer is rare for multiple families of prokaryotic insertion sequences

Molecular Genetics and Genomics

Volumn 280, Issue 5, 2008, Pages 397-408

  Wagner, Andreas ^a,b,c,d   De La Chaux, Nicole ^a,c  

^a UNIVERSITY OF ZURICH   (Switzerland)

^b SANTA FE INSTITUTE   (United States)

^c SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

^d UNIVERSITY OF NEW MEXICO   (United States)

Author keywords

Insertion sequences; Lateral gene transfer; Molecular evolution

Indexed keywords

DNA 16S; TRANSPOSASE;

ARTICLE; CONTROLLED STUDY; GENE INSERTION SEQUENCE; HORIZONTAL GENE TRANSFER; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; PROKARYOTE;

BACTERIAL PROTEINS; DNA, RIBOSOMAL; EVOLUTION, MOLECULAR; GENE TRANSFER, HORIZONTAL; GENOME, BACTERIAL; MUTAGENESIS, INSERTIONAL; PHYLOGENY; PROKARYOTIC CELLS; RNA, RIBOSOMAL, 16S;

PROKARYOTA;

EID: 54349125857     PISSN: 16174615     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00438-008-0373-y     Document Type: Article

References (80)

1. Ajioka J, Hartl D (1989) Population dynamics of transposable elements. In: Berg D, Howe M (eds) Mobile DNA. American Society for Microbiology Press, Washington, DC, pp 185-210
2. W Albritton 1989 Biology of Haemophilus ducreyi Microbiol Mol Biol Rev 53 377 389
3. Anderson R, May R (1991) Infectious diseases of humans. Dynamics and control. Oxford University Press, Oxford, UK
4. IR Arkhipova 2005 Mobile genetic elements and sexual reproduction Cytogenet Genome Res 110 372 382
5. C Bartolome X Maside B Charlesworth 2002 On the abundance and distribution of transposable elements in the genome of Drosophila melanogaster Mol Biol Evol 19 926 937
6. FR Blattner G Plunkett CA Bloch NT Perna V Burland M Riley J Colladovides JD Glasner CK Rode GF Mayhew J Gregor NW Davis HA Kirkpatrick MA Goeden DJ Rose B Mau Y Shao 1997 The complete genome sequence of Escherichia coli K-12 Science 277 1453 1474
7. M Blot 1994 Transposable elements and adaptation of host bacteria Genetica 93 5 12
8. JR Brown 2003 Ancient horizontal gene transfer Nat Rev Genet 4 121 132
9. K Brugger P Redder QX She F Confalonieri Y Zivanovic RA Garrett 2002 Mobile elements in archaeal genomes FEMS Microbiol Lett 206 131 141
10. P Capy G Gasperi C Biemont C Bazin 2000 Stress and transposable elements: co-evolution or useful parasites? Heredity 85 101 106
11. S Chaillou MC Champomier-Verges M Cornet AM Crutz-Le Coq AM Dudez V Martin S Beaufils E Darbon-Rongere R Bossy V Loux M Zagorec 2005 The complete genome sequence of the meat-borne lactic acid bacterium Lactobacillus sakei 23K Nat Biotechnol 23 1527 1533
12. B Charlesworth CH Langley 1989 The population genetics of Drosophila transposable elements Annu Rev Genet 23 251 287
13. B Charlesworth P Sniegowski W Stephan 1994 The evolutionary dynamics of repetitive DNA in eukaryotes Nature 371 215 220
14. IG Choi SH Kim 2007 Global extent of horizontal gene transfer Proc Natl Acad Sci USA 104 4489 4494
15. FD Ciccarelli T Doerks C von Mering CJ Creevey B Snel P Bork 2006 Toward automatic reconstruction of a highly resolved tree of life Science 311 1283 1287
16. GC Conant A Wagner 2002 GenomeHistory: a software tool and its applications to fully sequenced genomes Nucleic Acids Res 30 1 10
17. VS Cooper M Schneider M Blot RE Lenski 2001 Mechanisms causing rapid and parallel losses of ribose catabolism in evolving populations of Escherichia coli J Bacteriol 183 2834 2841
18. Craig N, Craigie R, Gellert M, Lambowitz AL (eds) (2002) Mobile DNA II. ASM Press, Washington, DC
19. V Daubin H Ochman 2004 Quartet mapping and the extent of lateral transfer in bacterial genomes Mol Biol Evol 21 86 89
20. V Daubin N Moran H Ochman 2003 Phylogenetics and the cohesion of bacterial genomes Science 301 829 832
21. F de la Cruz J Davies 2000 Horizontal gene transfer and the origin of species: lessons from bacteria Trends Microbiol 8 128 133
22. F Delsuc H Brinkmann H Philippe 2005 Phylogenomics and the reconstruction of the tree of life Nat Rev Genet 6 361 375
23. WF Doolittle 1999 Phylogenetic classification and the universal tree Science 284 2124 2128
24. WF Doolittle C Sapienza 1980 Selfish genes, the phenotype paradigm, and genome evolution Nature 284 601 607
25. RJ Edwards JFY Brookfield 2003 Transiently beneficial insertions could maintain mobile DNA sequences in variable environments Mol Biol Evol 20 30 37
26. EG Fingerman PG Dombrowski CA Francis PD Sniegowski 2003 Distribution and sequence analysis of a novel Ty3-like element in natural Saccharomyces paradoxus isolates Yeast 20 761 770
27. DJ Garfinkel 2005 Genome evolution mediated by Ty elements in Saccharomyces Cytogenet Genome Res 110 63 69
28. F Ge LS Wang J Kim 2005 The cobweb of life revealed by genome-scale estimates of horizontal gene transfer PLoS Biol 3 1709 1718
29. D Gevers FM Cohan JG Lawrence BG Spratt T Coenye EJ Feil E Stackebrandt Y Van de Peer P Vandamme FL Thompson J Swings 2005 Re-evaluating prokaryotic species Nat Rev Microbiol 3 733 739
30. D Godoy G Randle AJ Simpson DM Aanensen TL Pitt R Kinoshita BG Spratt 2003 Multilocus sequence typing and evolutionary relationships among the causative agents of melioidosis and glanders, Burkholderia pseudomallei and Burkholdefia mallei J Clin Microbiol 41 4913 (vol 41, pg 2068, 2003)
31. JP Gogarten WF Doolittle JG Lawrence 2002 Prokaryotic evolution in light of gene transfer Mol Biol Evol 19 2226 2238
32. S Guindon O Gascuel 2003 A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood Syst Biol 52 696 704
33. S Guindon O Gascuel 2003 A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood Syst Biol 52 696 704
34. DL Hartl DE Dykhuizen RD Miller J Green J de Framond 1983 Transposable element IS50 improves growth rate of E. coli cells without transposition Cell 35 503 510
35. M Hasegawa H Kishino TA Yano 1985 Dating of the human ape splitting by a molecular clock of mitochondria J Mol Evol 22 160 174
36. Higgs P, Attwood T (2005) Bioinformatics and molecular evolution. Blackwell, Oxford, UK
37. EV Koonin KS Makarova L Aravind 2001 Horizontal gene transfer in prokaryotes: Quantification and classification Annu Rev Microbiol 55 709 742
38. A Kotiranta K Lounatmaa M Haapasalo 2000 Epidemiology and pathogenesis of Bacillus cereus infections Microbes Infect 2 189 198
39. CG Kurland 2005 What tangled web: barriers to rampant horizontal gene transfer Bioessays 27 741 747
40. JA Lake R Jain MC Rivera 1999 Genomics-mix and match in the tree of life Science 283 2027 2028
41. JG Lawrence H Ochman 2002 Reconciling the many faces of lateral gene transfer Trends Microbiol 10 1 4
42. JG Lawrence H Ochman DL Hartl 1992 The evolution of insertion sequences within enteric bacteria Genetics 131 9 20
43. E Lerat V Daubin H Ochman NA Moran 2005 Evolutionary origins of genomic repertoires in bacteria PLoS Biol 3 e130
44. I Letunic P Bork 2007 Interactive tree of life (iTOL): an online tool for phylogenetic tree display and annotation Bioinformatics 23 127 128
45. Li W-H (1997) Molecular evolution. Sinauer, MA, USA
46. J Mahillon M Chandler 1998 Insertion sequences Microbiol Mol Biol Rev 62 725 774
47. X Maside S Assimacopoulos B Charlesworth 2000 Rates of movement of transposable elements on the second chromosome of Drosophila melanogaster Genet Res 75 275 284
48. X Maside S Assimacopoulos B Charlesworth 2005 Fixation of transposable elements in the Drosophila melanogaster genome Genet Res 85 195 203
49. T Naas M Blot WM Fitch W Arber 1994 Insertion sequence-related genetic variation in resting Escherichia coli K-12 Genetics 136 721 730
50. Z Nagy M Chandler 2004 Regulation of transposition in bacteria Res Microbiol 155 387 398
51. Y Nakamura T Itoh H Matsuda T Gojobori 2004 Biased biological functions of horizontally transferred genes in prokaryotic genomes Nat Genet 36 760 766
52. KE Nelson RA Clayton SR Gill ML Gwinn RJ Dodson DH Haft EK Hickey LD Peterson WC Nelson KA Ketchum L McDonald TR Utterback JA Malek KD Linher MM Garrett AM Stewart MD Cotton MS Pratt CA Phillips D Richardson J Heidelberg GG Sutton RD Fleischmann JA Eisen O White SL Salzberg HO Smith JC Venter CM Fraser 1999 Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima Nature 399 323 329
53. H Ochman J Lawrence E Groisman 2000 Lateral gene transfer and the nature of bacterial innovation Nature 405 299 304
54. H Ochman E Lerat V Daubin 2005 Examining bacterial species under the specter of gene transfer and exchange Proc Natl Acad Sci USA 102 6595 6599
55. LE Orgel FHC Crick 1980 Selfish DNA: the ultimate parasite Nature 284 604 607
56. EG Pasyukova SV Nuzhdin TV Morozova TFC Mackay 2004 Accumulation of transposable elements in the genome of Drosophila melanogaster is associated with a decrease in fitness J Hered 95 284 290
57. DA Petrov YT Aminetzach JC Davis D Bensasson AE Hirsh 2003 Size matters: non-LTR retrotransposable elements and ectopic recombination in Drosophila Mol Biol Evol 20 880 892
58. H Philippe CJ Douady 2003 Horizontal gene transfer and phylogenetics Curr Opin Microbiol 6 498 505
59. MA Ragan 2001 Detection of lateral gene transfer among microbial genomes Curr Opin Genet Dev 11 620 626
60. Ryan K, Ray C (eds) (2004) Sherris medical microbiology. McGraw Hill, New York
61. A Sanchez-Gracia X Maside B Charlesworth 2005 High rate of horizontal transfer of transposable elements in Drosophila Trends Genet 21 200 203
62. S Sawyer DL Hartl 1986 Distribution of transposable elements in prokaryotes Theor Popul Biol 30 1 16
63. D Schneider RE Lenski 2004 Dynamics of insertion sequences elements during experimental evolution of bacteria Res Microbiol 155 319 327
64. P Siguier J Filee M Chandler 2006 Insertion sequences in prokaryotic genomes Curr Opin Microbiol 9 526 531
65. P Siguier J Perochon L Lestrade J Mahillon M Chandler 2006 ISfinder: the reference centre for bacterial insertion sequences Nucleic Acids Res (Database issue) 34 D34 D36
66. B Snel P Bork MA Huynen 1999 Genome phylogeny based on gene content Nat Genet 21 108 110
67. R Sorek YX Zhu C Creevey M Francino P Bork E Rubin 2007 Genome-wide experimental determination of barriers to horizontal gene transfer Science 318 5855 1449 1452
68. CM Thomas KM Nielsen 2005 Mechanisms of, and barriers to, horizontal gene transfer between bacteria Nat Rev Microbiol 3 711 721
69. JD Thompson DG Higgins TJ Gibson 1994 Clustal-W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting; position-specific gap penalties and weight matrix choice Nucleic Acids Res 22 4673 4680
70. MA Toleman PM Bennett TR Walsh 2006 ISCR elements: novel gene-capturing systems of the 21st century? Microbiol Mol Biol Rev 70 2 296 316
71. M Touchon EPC Rocha 2007 Causes of insertion sequences abundance in prokaryotic genomes Mol Biol Evol 24 969 981
72. DS Treves S Manning J Adams 1998 Repeated evolution of an acetate-crossfeeding polymorphism in long-term populations of Escherichia coli Mol Biol Evol 15 789 797
73. C Vieira C Biemont 2004 Transposable element dynamics in two sibling species: Drosophila melanogaster and Drosophila simulans Genetica 120 115 123
74. C Vieira C Nardon C Arpin D Lepetit C Biemont 2002 Evolution of genome size in Drosophila. Is the invader's genome being invaded by transposable elements? Mol Biol Evol 19 1154 1161
75. RM Vonsternberg GE Novick GP Gao RJ Herrera 1992 Genome canalization: the coevolution of transposable and interspersed repetitive elements with single copy DNA Genetica 86 215 246
76. A Wagner 2006 Periodic extinctions of transposable elements in bacterial lineages: evidence from intragenomic variation in multiple genomes Mol Biol Evol 23 723 733
77. A Wagner C Lewis M Bichsel 2007 A survey of bacterial insertion sequences using IScan Nucleic Acids Res 35 5284 5293
78. CM Wilke J Adams 1992 Fitness effects of Ty transposition in Saccharomyces cerevisiae Genetics 131 31 42
79. DJ Witherspoon HM Robertson 2003 Neutral evolution of ten types of mariner transposons in the genomes of Caenorhabditis elegans and Caenorhabditis briggsae J Mol Evol 56 751 769
80. C Zeyl G Bell DM Green 1996 Sex and the spread of retrotransposon Ty3 in experimental populations of Saccharomyces cerevisiae Genetics 143 1567 1577