The evolutionary origin of Xanthomonadales genomes and the nature of the horizontal gene transfer process

Molecular Biology and Evolution

Volumn 23, Issue 11, 2006, Pages 2049-2057

  Comas, Iñaki ^a,b   Moya, Andrés ^a   Azad, Rajeev K ^b   Lawrence, Jeffrey G ^b   Gonzalez Candelas, Fernando ^a  

^a UNIVERSITY OF VALENCIA   (Spain)

^b UNIVERSITY OF PITTSBURGH   (United States)

Author keywords

Conflicting phylogenetic signals; Horizontal gene transfer; Microbial evolution; Phylogenomics

Indexed keywords

ARTICLE; BACTERIAL GENOME; EVOLUTION; GENE MAPPING; HORIZONTAL GENE TRANSFER; NONHUMAN; PHYLOGENETIC TREE; PHYLOGENY; PROTEOBACTERIA; SIGNAL NOISE RATIO; XANTHOMONADALES;

CLUSTER ANALYSIS; EVOLUTION, MOLECULAR; GENE TRANSFER, HORIZONTAL; GENOME, BACTERIAL; PHYLOGENY; XANTHOMONADACEAE;

BACTERIA (MICROORGANISMS); PROTEOBACTERIA; XANTHOMONADALES;

EID: 33749554389     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msl075     Document Type: Article

References (38)

1. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389-402.
2. Azad RK, Lawrence JG. 2005. Use of artificial genomes in assessing methods for atypical gene detection. PLoS Comput Biol 1:e56.
3. Bapteste E, Susko E, Leigh J, MacLeod D, Charlebois RL, Doolittle WF. 2005. Do orthologous gene phylogenies really support tree-thinking? BMC Evol Biol 5:33.
4. Beiko RG, Harlow TJ, Ragan MA. 2005. Highways of gene sharing in prokaryotes. Proc Natl Acad Sci USA 102:14332-7.
5. Bern M, Goldberg D. 2005. Automatic selection of representative proteins for bacterial phylogeny. BMC Evol Biol 5:34.
6. Boucher Y, Douady CJ, Papke RT, Walsh DA, Boudreau MER, Nesbo CL, Case RJ, Doolittle WF. 2003. Lateral gene transfer and the origins of prokaryotic groups. Annu Rev Genet 37:283-328.
7. Charlebois RL, Clarke GDP, Beiko RG, Jean A. 2003. Characterization of species-specific genes using a flexible, web-based querying system. FEMS Microbiol Lett 225:213-20.
8. Creevey CJ, Fitzpatrick DA, Philip GK, Kinsella RJ, O'Connell MJ, Pentony MM, Travers SA, Wilkinson M, McInerney JO. 2004. Does a tree-like phylogeny only exist at the tips in the prokaryotes? Proc R Soc Lond B Biol Sci 271:2551-8.
9. Darling ACE, Mau B, Blattner FR, Perna NT. 2004. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res 14:1394-403.
10. Doolittle WF. 1999. Phylogenetic classification and the universal tree. Science 284:2124-8.
11. Dutilh BE, Huynen MA, Bruno WJ, Snel B. 2005. The consistent phylogenetic signal in genome trees revealed by reducing the impact of noise. J Mol Evol 58:527-39.
12. Gogarten JP, Doolittle WF, Lawrence JG. 2002. Prokaryotic evolution in light of gene transfer. Mol Biol Evol 19:2226-38.
13. Guindon S, Gascuel O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52:696-704.
14. Hauck B, Gehring WJ, Walldorf U. 1999. Functional analysis of an eye specific enhancer of the eyeless gene in Drosophila. Proc Natl Acad Sci USA 96:564-9.
15. Hendrickson H, Lawrence JG. 2006. Selection for chromosome architecture in bacteria. J Mol Evol 62:615-29.
16. Jain R, Rivera MC, Lake JA. 1999. Horizontal gene transfer among genomes: the complexity hypothesis. Proc Natl Acad Sci USA 96:3801-6.
17. Jones DT, Taylor WR, Thornton JM. 1994. A mutation data matrix for transmembrane proteins. FEBS Lett 339:269-75.
18. Koonin EV, Galperin MY. 1997. Prokaryotic genomes: the emerging paradigm of genome-based microbiology. Curr Opin Genet Dev 7:757-63.
19. Koonin EV, Makarova KS, Aravind L. 2001. Horizontal gene transfer in prokaryotes: quantification and classification. Annu Rev Microbiol 55:709-42.
20. Kunin V, Goldovsky L, Darzentas N, Ouzounis CA. 2005. The net of life: reconstructing the microbial phylogenetic network. Genome Res 15:954-9.
21. Lawrence JG, Hendrickson H. 2003. Lateral gene transfer: when will adolescence end? Mol Microbiol 50:739-49.
22. Lawrence JG, Hendrickson H. 2004. Chromosome structure and constraints on lateral gene transfer. Dynamical Genet 2004:319-36.
23. Lawrence JG, Ochman H. 2002. Reconciling the many faces of lateral gene transfer. Trends Microbiol 10:1-4.
24. Lawrence JG, Roth JR. 1996. Selfish operons: horizontal transfer may drive the evolution of gene clusters. Genetics 143:1843-60.
25. Martins-Pinheiro M, Galhardo RS, Aires KA, Lima-Bessa KM, Menck CFM. 2004. Different patterns of evolution for duplicated DNA repair genes in bacteria of the Xanthomonadales group. BMC Evol Biol 4:29.
26. Nakamura Y, Itoh T, Matsuda H, Gojobori T. 2004. Biased biological functions of horizontally transferred genes in prokaryotic genomes. Nat Genet 36:760-6.
27. Ochman H, Lawrence JG, Groisman EA. 2000. Lateral gene transfer and the nature of bacterial innovation. Nature 405:299-304.
28. Omelchenko M, Makarova K, Wolf Y, Rogozin I, Koonin E. 2003. Evolution of mosaic operons by horizontal gene transfer and gene displacement in situ. Genome Biol 4:R55.
29. Pal C, Papp B, Lercher MJ. 2005. Adaptive evolution of bacterial metabolic networks by horizontal gene transfer. Nat Genet 37:1372-5.
30. Robinson-Rechavi M, Huchon D. 2000. RRTree: relative-rate tests between groups of sequences on a phylogenetic tree. Bioinformatics 16:296-7.
31. Snel B, Huynen MA, Dutilh BE. 2005. Genome trees and the nature of genome evolution. Annu Rev Microbiol 59:191-209.
32. Strimmer K, Rambaut A. 2002. Inferring confidence sets of possibly misspecified gene trees. Proc R Soc Lond B Biol Sci 269:137-42.
33. Studholme DJ, Downie JA, Preston GM. 2005. Protein domains and architectural innovation in plant-associated Proteobacteria. BMC Genomics 6:17.
34. Susko E, Leigh J, Doolittle WF, Bapteste E. 2006. Visualizing and assessing phylogenetic congruence of core gene sets: a case study of the c-Proteobacteria. Mol Biol Evol 23:1019-30.
35. Tamas I, Klasson L, Canback B, Naslund AK, Eriksson AS, Wernegreen JJ, Sandstrom JP, Moran NA, Andersson SGE. 2002. 50 million years of genomic stasis in endosymbiotic bacteria. Science 296:2376-9.
36. Tatusov RL, Galperin MY, Natale DA, Koonin EV. 2000. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 28:33-6.
37. Tettelin H, Masignani V, Cieslewicz MJ, et al. (36 co-authors). 2005. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome." Proc Natl Acad Sci USA 102:13950-5.
38. Van Sluys MA, Monteiro-Vitorello CB, Camargo LEA, Menck CFM, da Silva ACR, Ferro JA, Oliveira MC, Setubal JC, Kitajima JP, Simpson AJ. 2002. Comparative genomic analysis of plant-associated bacteria. Annu Rev Phytopathol 40:169-89.