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Detection and Quantitative Assessment of Horizontal Gene Transfer

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Book cover Horizontal Gene Transfer

Part of the book series: Methods in Molecular Biology ((MIMB,volume 532))

Abstract

This chapter discusses the pros and cons of the existing computational methods for the detection of horizontal (or lateral) gene transfer and highlights the genome-wide studies utilizing these methods. The impact of horizontal gene transfer (HGT) on prokaryote genome evolution is discussed.

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References

  1. iolios, K., Mavromatis, K., Tavernarakis, N., Kyrpides, N. C. (2007) The genomes on line database (GOLD) in 2007: Status of genomic and metagenomic projects and their associated metadata. Nucl Acids Res 36, D475–D479.

    Article  Google Scholar 

  2. agan, M. A. (2001) Detection of lateral gene transfer among microbial genomes. Curr Opin Genet Dev 11, 620–6.

    Article  Google Scholar 

  3. agan, M. A. (2002) Reconciling the many faces of lateral gene transfer. Trends Microbiol 10, 4.

    Article  Google Scholar 

  4. agan, M. A., Harlow, T. J., Beiko, R. G. (2006) Do different surrogate methods detect lateral genetic transfer events of different relative ages? Trends Microbiol 14, 4–8.

    Article  Google Scholar 

  5. awrence, J. G., Ochman, H. (1997) Amelioration of bacterial genomes: Rates of change and exchange. J Mol Evol 44, 383–97.

    Article  Google Scholar 

  6. ortez, D. Q., Lazcano, A., Becerra, A. (2005) Comparative analysis of methodologies for the detection of horizontally transferred genes: A reassessment of first-order Markov models. In Silico Biol 5, 0052.

    Google Scholar 

  7. optsova, M. S., Gogarten, J. P. (2007) The power of phylogenetic approaches to detect horizontally transferred genes. BMC Evol Biol 7, 45.

    Article  Google Scholar 

  8. haxybayeva, O., Gogarten, J. P., Charlebois, R. L., Doolittle, W. F., Papke, R. T. (2006) Phylogenetic analyses of cyanobacterial genomes: Quantification of horizontal gene transfer events. Genome Res 16, 1099–108.

    Article  Google Scholar 

  9. eiko, R. G., Charlebois, R. L. (2007) A simulation test bed for hypotheses of genome evolution. Bioinformatics 23, 825–31.

    Article  Google Scholar 

  10. Karlin, S. (2001) Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial genomes. Trends Microbiol 9, 335–43.

    Article  CAS  PubMed  Google Scholar 

  11. Putonti, C., Luo, Y., Katili, C., Chumakov, S., Fox, G. E., Graur, D., Fofanov, Y. (2006) A computational tool for the genomic identification of regions of unusual compositional properties and its utilization in the detection of horizontally transferred sequences. Mol Biol Evol 23, 1863–8.

    Article  CAS  PubMed  Google Scholar 

  12. Van Passel, M. W. J., Bart, A., Thygesen, H. H., Luyf, A. C. M., Van Kampen, A. H. C., Van Der Ende, A. (2005) An acquisition account of genomic islands based on genome signature comparisons. BMC Genomics 6, 163.

    Article  PubMed  Google Scholar 

  13. Lawrence, J. G., Ochman, H. (1998) Molecular archaeology of the Escherichia coli genome. Proc Natl Acad Sci U S A 95, 9413–7.

    Article  CAS  PubMed  Google Scholar 

  14. Tsirigos, A., Rigoutsos, I. (2005) A new computational method for the detection of horizontal gene transfer events. Nucl Acids Res 33, 922–33.

    Article  CAS  PubMed  Google Scholar 

  15. Koski, L. B., Morton, R. A., Golding, G. B. (2001) Codon bias and base composition are poor indicators of horizontally transferred genes. Mol Biol Evol 18, 404–12.

    CAS  PubMed  Google Scholar 

  16. Azad, R. K., Lawrence, J. G. (2005) Use of artificial genomes in assessing methods for atypical gene detection. PLoS Comput Biol 1, e56.

    Article  PubMed  Google Scholar 

  17. Nakamura, Y., Itoh, T., Matsuda, H., Gojobori, T. (2004) Biased biological functions of horizontally transferred genes in prokaryotic genomes. Nat Genet 36, 760–6.

    Article  CAS  PubMed  Google Scholar 

  18. Hsiao, W. W. L., Ung, K., Aeschliman, D., Bryan, J., Finlay, B. B., Brinkman, F. S. L. (2005) Evidence of a large novel gene pool associated with prokaryotic genomic islands. PLoS Genet 1, e62.

    Article  PubMed  Google Scholar 

  19. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W., Lipman, D. J. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 25, 3389–402.

    Article  CAS  PubMed  Google Scholar 

  20. Nelson, K. E., Clayton, R. A., Gill, S. R., Gwinn, M. L., Dodson, R. J., Haft, D. H., Hickey, E. K., Peterson, J. D., Nelson, W. C., Ketchum, K. A., Mcdonald, L., Utterback, T. R., Malek, J. A., Linher, K. D., Garrett, M. M., Stewart, A. M., Cotton, M. D., Pratt, M. S., Phillips, C. A., Richardson, D., Heidelberg, J., Sutton, G. G., Fleischmann, R. D., Eisen, J. A., White, O., Salzberg, S. L., Smith, H. O., Venter, J. C., Fraser, C. M. (1999) Evidence for lateral gene transfer between archaea and bacteria from genome sequence of Thermotoga maritima. Nature 399, 323–9.

    Article  CAS  PubMed  Google Scholar 

  21. Koski, L. B., Golding, G. B. (2001) The closest BLAST hit is often not the nearest neighbor. J Mol Evol 52, 540–2.

    CAS  PubMed  Google Scholar 

  22. Podell, S., Gaasterland, T. (2007) Darkhorse: A method for genome-wide prediction of horizontal gene transfer. Genome Biol 8, R16.

    Article  PubMed  Google Scholar 

  23. Welch, R. A., Burland, V., Plunkett, G., Iii, Redford, P., Roesch, P., Rasko, D., Buckles, E. L., Liou, S. R., Boutin, A., Hackett, J., Stroud, D., Mayhew, G. F., Rose, D. J., Zhou, S., Schwartz, D. C., Perna, N. T., Mobley, H. L. T., Donnenberg, M. S., Blattner, F. R. (2002) Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli. PNAS 99, 17020–4.

    Article  CAS  PubMed  Google Scholar 

  24. Normand, P., Lapierre, P., Tisa, L. S., Gogarten, J. P., Alloisio, N., Bagnarol, E., Bassi, C. A., Berry, A. M., Bickhart, D. M., Choisne, N., Couloux, A., Cournoyer, B., Cruveiller, S., Daubin, V., Demange, N., Francino, M. P., Goltsman, E., Huang, Y., Kopp, O. R., Labarre, L., Lapidus, A., Lavire, C., Marechal, J., Martinez, M., Mastronunzio, J. E., Mullin, B. C., Niemann, J., Pujic, P., Rawnsley, T., Rouy, Z., Schenowitz, C., Sellstedt, A., Tavares, F., Tomkins, J. P., Vallenet, D., Valverde, C., Wall, L. G., Wang, Y., Medigue, C., Benson, D. R. (2007) Genome characteristics of facultatively symbiotic Frankia sp. Strains reflect host range and host plant biogeography. Genome Res 17, 7–15.

    Article  PubMed  Google Scholar 

  25. Kunin, V., Ouzounis, C. A. (2003) GeneTRACE-reconstruction of gene content of ancestral species. Bioinformatics 19, 1412–6.

    Article  CAS  PubMed  Google Scholar 

  26. Mirkin, B. G., Fenner, T. I., Galperin, M. Y., Koonin, E. V. (2003) Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes. BMC Evol Biol 3, 2.

    Article  PubMed  Google Scholar 

  27. Snel, B., Bork, P., Huynen, M. A. (2002) Genomes in flux: The evolution of archaeal and proteobacterial gene content. Genome Res 12, 17–25.

    Article  CAS  PubMed  Google Scholar 

  28. Zhaxybayeva, O., Nesb π, C. L., Doolittle, W. F. (2007) Systematic overestimation of gene gain through false diagnosis of gene absence. Genome Biol 8, 402.

    Article  PubMed  Google Scholar 

  29. Novichkov, P. S., Omelchenko, M. V., Gelfand, M. S., Mironov, A. A., Wolf, Y. I., Koonin, E. V. (2004) Genome-wide molecular clock and horizontal gene transfer in bacterial evolution. J Bacteriol 186, 6575–85.

    Article  CAS  PubMed  Google Scholar 

  30. Hamady, M., Betterton, M. D., Knight, R. (2006) Using the nucleotide substitution rate matrix to detect horizontal gene transfer. BMC Bioinformatics 7, 476.

    Article  PubMed  Google Scholar 

  31. Deckert, G., Warren, P. V., Gaasterland, T., Young, W. G., Lenox, A. L., Graham, D. E., Overbeek, R., Snead, M. A., Keller, M., Aujay, M., Huber, R., Feldman, R. A., Short, J. M., Olsen, G. J., Swanson, R. V. (1998) The complete genome of the hyperthermophilic bacterium AQUIFEX AEOLICUS. Nature 392, 353.

    Article  CAS  PubMed  Google Scholar 

  32. Lerat, E., Daubin, V., Moran, N. A. (2003) From gene trees to organismal phylogeny in prokaryotes: The case of the gamma-proteobacteria. PLoS Biol 1, E19.

    Article  PubMed  Google Scholar 

  33. Beiko, R. G., Harlow, T. J., Ragan, M. A. (2005) Highways of gene sharing in prokaryotes. Proc Natl Acad Sci U S A 102, 14332–7.

    Article  CAS  PubMed  Google Scholar 

  34. Macleod, D., Charlebois, R., Doolittle, F., Bapteste, E. (2005) Deduction of probable events of lateral gene transfer through comparison of phylogenetic trees by recursive consolidation and rearrangement. BMC Evolutionary Biology 5, 27.

    Article  PubMed  Google Scholar 

  35. Makarenkov, V. (2001) T-REX: Reconstructing and visualizing phylogenetic trees and reticulation networks. Bioinformatics 17, 664–8.

    Article  CAS  PubMed  Google Scholar 

  36. Beiko, R., Hamilton, N. (2006) Phylogenetic identification of lateral genetic transfer events. BMC Evolutionary Biology 6, 15.

    Article  PubMed  Google Scholar 

  37. Hamel, L., Zhaxybayeva, O., Gogarten, J. P. (2005) Pentaplot: A software tool for the illustration of genome mosaicism. BMC Bioinformatics 6, 139.

    Article  PubMed  Google Scholar 

  38. Zhaxybayeva, O., Gogarten, J. (2002) Bootstrap, Bayesian probability and maximum likelihood mapping: Exploring new tools for comparative genome analyses. BMC Genomics 3, 4.

    Article  PubMed  Google Scholar 

  39. Zhaxybayeva, O., Hamel, L., Raymond, J., Gogarten, J. (2004) Visualization of the phylogenetic content of five genomes using dekapentagonal maps. Genome Biol 5, R20.

    Article  PubMed  Google Scholar 

  40. Bapteste, E., Susko, E., Leigh, J., Macleod, D., Charlebois, R. L., Doolittle, W. F. (2005) Do orthologous gene phylogenies really support tree-thinking? BMC Evol Biol 5, 33.

    Article  CAS  PubMed  Google Scholar 

  41. Zhaxybayeva, O., Lapierre, P., Gogarten, J. P. (2004) Genome mosaicism and organismal lineages. Trends Genet 20, 254–60.

    Article  CAS  PubMed  Google Scholar 

  42. Felsenstein, J. (1988) Phylogenies from molecular sequences: Inference and reliability. Annu Rev Genet 22, 521–65.

    Article  CAS  PubMed  Google Scholar 

  43. Zhaxybayeva, O., Gogarten, J. P. (2003) An improved probability mapping approach to assess genome mosaicism. BMC Genomics 4, 37.

    Article  PubMed  Google Scholar 

  44. Lento, G. M., Hickson, R. E., Chambers, G. K., Penny, D. (1995) Use of spectral analysis to test hypotheses on the origin of pinnipeds. Mol Biol Evol 12, 28–52.

    CAS  PubMed  Google Scholar 

  45. Wainright, P. O., Hinkle, G., Sogin, M. L., Stickel, S. K. (1993) Monophyletic origins of the metazoa: An evolutionary link with fungi. Science 260, 340–2.

    Article  CAS  PubMed  Google Scholar 

  46. Than, C., Ruths, D., Innan, H., Nakhleh, L. (2007) Confounding factors in HGT detection: Statistical error, coalescent effects, and multiple solutions. J Comput Biol 14, 517–35.

    Article  CAS  PubMed  Google Scholar 

  47. Galtier, N. (2007) A model of horizontal gene transfer and the bacterial phylogeny problem. Syst Biol 56, 633–42.

    Article  PubMed  Google Scholar 

  48. Degnan, J. H., Rosenberg, N. A. (2006) Discordance of species trees with their most likely gene trees. PLoS Genet 2, e68.

    Article  PubMed  Google Scholar 

  49. Mau, B., Glasner, J., Darling, A., Perna, N. (2006) Genome-wide detection and analysis of homologous recombination among sequenced strains of Escherichia coli. Genome Biol 7, R44.

    Article  PubMed  Google Scholar 

  50. Charlebois, R. L., Doolittle, W. F. (2004) Computing prokaryotic gene ubiquity: Rescuing the core from extinction. Genome Res 14, 2469–77.

    Article  CAS  PubMed  Google Scholar 

  51. Ciccarelli, F. D., Doerks, T., Von Mering, C., Creevey, C. J., Snel, B., Bork, P. (2006) Toward automatic reconstruction of a highly resolved tree of life. Science 311, 1283–7.

    Article  CAS  PubMed  Google Scholar 

  52. Dagan, T., Martin, W. (2006) The tree of one percent. Genome Biol 7, 118.

    Article  PubMed  Google Scholar 

  53. Choi, I.-G., Kim, S.-H. (2007) Global extent of horizontal gene transfer. Proc Natl Acad Sci U S A 104, 4489–94.

    Article  CAS  PubMed  Google Scholar 

  54. Ge, F., Wang, L.-S., Kim, J. (2005) The cobweb of life revealed by genome-scale estimates of horizontal gene transfer. PLoS Biol 3, e316.

    Article  PubMed  Google Scholar 

  55. Dagan, T., Martin, W. (2007) Ancestral genome sizes specify the minimum rate of lateral gene transfer during prokaryote evolution. Proc Natl Acad Sci U S A 104, 870–5.

    Article  CAS  PubMed  Google Scholar 

  56. Doolittle, W. F., Boucher, Y., Nesbo, C. L., Douady, C. J., Andersson, J. O., Roger, A. J. (2003) How big is the iceberg of which organellar genes in nuclear genomes are but the tip? Philos Trans R Soc Lond B Biol Sci 358, 39–57.

    Article  CAS  PubMed  Google Scholar 

  57. Suchard, M. A. (2005) Stochastic models for horizontal gene transfer: Taking a random walk through tree space. Genetics 170, 419–31.

    Article  CAS  PubMed  Google Scholar 

  58. Linz, S., Radtke, A., Von Haeseler, A. (2007) A likelihood framework to measure horizontal gene transfer. Mol Biol Evol 24, 1312–9.

    Article  CAS  PubMed  Google Scholar 

  59. Jain, R., Rivera, M. C., Lake, J. A. (1999) Horizontal gene transfer among genomes: The complexity hypothesis. Proc Natl Acad Sci U S A 96, 3801–6.

    Article  CAS  PubMed  Google Scholar 

  60. Huson, D. H., Bryant, D. (2006) Application of phylogenetic networks in evolutionary studies. Mol Biol Evol 23, 254–67.

    Article  CAS  PubMed  Google Scholar 

  61. Swingley, W. D., Blankenship, R. E., Raymond, J. (2008) Integrating Markov clustering and molecular phylogenetics to reconstruct the cyanobacterial species tree from conserved protein families. Mol Biol Evol 25, 643–54.

    Article  CAS  PubMed  Google Scholar 

  62. Harlow, T. J., Gogarten, J. P., Ragan, M. A. (2004) A hybrid clustering approach to recognition of protein families in 114 microbial genomes. BMC Bioinform 5, 45.

    Article  Google Scholar 

  63. Poptsova, M. S., Gogarten, J. P. (2007) BranchClust: A phylogenetic algorithm for selecting gene families. BMC Bioinform 8, 120.

    Article  Google Scholar 

  64. Larkin, M. A., Blackshields, G., Brown, N. P., Chenna, R., Mcgettigan, P. A., Mcwilliam, H., Valentin, F., Wallace, I. M., Wilm, A., Lopez, R., Thompson, J. D., Gibson, T. J., Higgins, D. G. (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23, 2947–8.

    Article  CAS  PubMed  Google Scholar 

  65. Edgar, R. C. (2004) Muscle: Multiple sequence alignment with high accuracy and high throughput. Nucl Acids Res 32, 1792–7.

    Article  CAS  PubMed  Google Scholar 

  66. Golubchik, T., Wise, M. J., Easteal, S., Jermiin, L. S. (2007) Mind the gaps: Evidence of bias in estimates of multiple sequence alignments. Mol Biol Evol 24, 2433–42.

    Article  CAS  PubMed  Google Scholar 

  67. Landan, G., Graur, D. (2007) Heads or tails: A simple reliability check for multiple sequence alignments. Mol Biol Evol 24, 1380–3.

    Article  CAS  PubMed  Google Scholar 

  68. Talavera, G., Castresana, J. (2007) Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol 56, 564–77.

    Article  CAS  PubMed  Google Scholar 

  69. Wong, K. M., Suchard, M. A., Huelsenbeck, J. P. (2008) Alignment uncertainty and genomic analysis. Science 319, 473–6.

    Article  CAS  PubMed  Google Scholar 

  70. Felsenstein, J. (1993) PHYLIP (phylogeny inference package) version 3.6. Distributed by the author. Department of Genetics, University of Washington, Seattle.

    Google Scholar 

  71. Guindon, S., Gascuel, O. (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52, 696–704.

    Article  PubMed  Google Scholar 

  72. Stamatakis, A. (2006) RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22, 2688–90.

    Article  CAS  PubMed  Google Scholar 

  73. Chase, P. (1970) Algorithm 382: Combinations of m out of n objects [g6]. Commun ACM 13, 368.

    Article  Google Scholar 

  74. Quartet suite 1.0 (2007) (Accessed at http://genome.cs.iastate.edu/CBL/download/ genome.cs.iastate.edu/CBL/download/).

  75. Baum, B. (1992) Combining trees as a way of combining data sets for phylogenetic inference, and the desirability of combining gene trees. Taxon 41, 3–10.

    Article  Google Scholar 

  76. Ragan, M. A. (1992) Phylogenetic inference based on matrix representation of trees. Mol Phylogenet Evol 1, 53–8.

    Article  CAS  PubMed  Google Scholar 

  77. Creevey, C. J., Mcinerney, J. O. (2005) Clann: Investigating phylogenetic information through supertree analyses. Bioinformatics 21, 390–2.

    Article  CAS  PubMed  Google Scholar 

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Author information

Authors and Affiliations

  1. Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada

    Olga Zhaxybayeva

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  1. Olga Zhaxybayeva
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Editors and Affiliations

  1. University of Connecticut, 968 Warrenville Road, Mansfield Center, CT 06250, USA

    Maria Boekels Gogarten

  2. Dept. Molecular & Cell Biology, University of Connecticut, 91 North Eagleville Rd., Storrs, CT 06269-3125, USA

    Johann Peter Gogarten

  3. Biology Department, St. Lawrence University, 23 Romoda Drive, Canton, NY 13617, USA

    Lorraine C. Olendzenski

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Zhaxybayeva, O. (2009). Detection and Quantitative Assessment of Horizontal Gene Transfer. In: Gogarten, M.B., Gogarten, J.P., Olendzenski, L.C. (eds) Horizontal Gene Transfer. Methods in Molecular Biology, vol 532. Humana Press. https://doi.org/10.1007/978-1-60327-853-9_11

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  • DOI: https://doi.org/10.1007/978-1-60327-853-9_11

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-60327-852-2

  • Online ISBN: 978-1-60327-853-9

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