Ancient horizontal gene transfer can benefit phylogenetic reconstruction

Trends in Genetics

Volumn 22, Issue 7, 2006, Pages 361-366

  Huang, Jinling ^a,b,c   Gogarten, Johann Peter ^b  

^a EAST CAROLINA UNIVERSITY   (United States)

^b UNIVERSITY OF CONNECTICUT   (United States)

^c MARINE BIOLOGICAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FLORFENICOL;

AMINO ACID SEQUENCE; ANIMAL GENETICS; ARCHAEBACTERIUM; ARTICLE; BACTERIAL GENE; BACTERIAL GENETICS; BACTERIUM; DELTAPROTEOBACTERIA; ENDOSYMBIOSIS; EUKARYOTE; EVOLUTIONARY HOMOLOGY; FUNGAL GENE; GENE DUPLICATION; GENE TRANSFER; GENETIC CORRELATION; GENETIC SIMILARITY; GENOME ANALYSIS; GREEN ALGA; HOMOLOGOUS RECOMBINATION; HORIZONTAL GENE TRANSFER; HUMAN; MARKER GENE; MAXIMUM LIKELIHOOD METHOD; MOLECULAR EVOLUTION; MOLECULAR PHYLOGENY; NONHUMAN; PLANT GENETICS; PRIORITY JOURNAL; RED ALGA; SEQUENCE HOMOLOGY; VERTICAL TRANSMISSION;

AMINO ACID SEQUENCE; ANIMALS; COMPUTATIONAL BIOLOGY; DNA TOPOISOMERASE IV; EVOLUTION, MOLECULAR; GENE TRANSFER, HORIZONTAL; GENOME, ARCHAEAL; GENOME, BACTERIAL; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PHYLOGENY;

RHODOPHYTA; VIRIDIPLANTAE;

EID: 33745760575     PISSN: 01689525     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tig.2006.05.004     Document Type: Article

References (58)

1. Ochman H., et al. Lateral gene transfer and the nature of bacterial innovation. Nature 405 (2000) 299-304
2. Gogarten J.P., et al. Prokaryotic evolution in light of gene transfer. Mol. Biol. Evol. 19 (2002) 2226-2238
3. Dobrindt U., et al. Genomic islands in pathogenic and environmental microorganisms. Nat. Rev. Microbiol. 2 (2004) 414-424
4. Andersson J.O. Lateral gene transfer in eukaryotes. Cell. Mol. Life Sci. 62 (2005) 1182-1197
5. Zhaxybayeva O., et al. Genome mosaicism and organismal lineages. Trends Genet. 20 (2004) 254-260
6. Philippe H., and Douady C.J. Horizontal gene transfer and phylogenetics. Curr. Opin. Microbiol. 6 (2003) 498-505
7. Doolittle W.F. Phylogenetic classification and the universal tree. Science 284 (1999) 2124-2129
8. Jain R., et al. Horizontal gene transfer among genomes: the complexity hypothesis. Proc. Natl. Acad. Sci. U. S. A. 96 (1999) 3801-3806
9. Huang J., et al. Phylogenomic evidence supports past endosymbiosis, intracellular and horizontal gene transfer in Cryptosporidium parvum. Genome Biol. 5 (2004) R88
10. Loftus B., et al. The genome of the protist parasite Entamoeba histolytica. Nature 433 (2005) 865-868
11. Huang J., et al. The presence of a haloarchaeal tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic. Mol. Biol. Evol. 22 (2005) 2142-2146
12. Smith M.W., et al. Evolution by acquisition: the case for horizontal gene transfers. Trends Biochem. Sci. 17 (1992) 489-493
13. Gray M.W. Origin and evolution of organelle genomes. Curr. Opin. Genet. Dev. 3 (1993) 884-890
14. Hilario E., and Gogarten J.P. Horizontal transfer of ATPase genes-the tree of life becomes a net of life. Biosystems 31 (1993) 111-119
15. Gogarten J.P., et al. Gene duplications and horizontal gene transfer during early evolution. In: Roberts D., et al. (Ed). Evolution of Microbial Life (1996), Cambridge Univ. Press 267-292
16. Gogarten J.P., et al. Horizontal gene transfer: pitfalls and promises. Biol. Bull. 196 (1999) 359-362
17. Bapteste E., et al. Phylogenetic reconstruction and lateral gene transfer. Trends Microbiol. 12 (2004) 406-411
18. Doolittle W.F. You are what you eat: a gene transfer ratchet could account for bacterial genes in eukaryotic nuclear genomes. Trends Genet. 14 (1998) 307-311
19. Woese C.R., et al. Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process. Microbiol. Mol. Biol. Rev. 64 (2000) 202-236
20. Doolittle W.F. Lateral genomics. Trends Cell Biol. 9 (1999) 5-8
21. Katz L.A. The tangled web: gene genealogies and the origin of eukaryotes. Am. Nat. 154 (1999) S137-S145
22. Kunin V., et al. The net of life: reconstructing the microbial phylogenetic network. Genome Res. 15 (2005) 954-959
23. Baldauf S.L., and Palmer J.D. Animals and fungi are each other's closest relatives: congruent evidence from multiple proteins. Proc. Natl. Acad. Sci. U. S. A. 90 (1993) 11558-11562
24. Wainright P.O. Monophyletic origins of the metazoa: an evolutionary link with fungi. Science 260 (1993) 340-342
25. Lang B.F., et al. The closest unicellular relatives of animals. Curr. Biol. 12 (2002) 1773-1778
26. Stiller J.W. Emerging genomic and proteomic evidence on relationships among the animal, plant and fungal kingdoms. Genomics Proteomics Bioinformatics 2 (2004) 70-76
27. Philip G.K., et al. The ophisthokonta and the ecdysozoa may not be clades: stronger support for the grouping of plant and animal than for animal and fungi and stronger support for the coelomata than ecdysozoa. Mol. Biol. Evol. 22 (2005) 1175-1184
28. Andersson J.O., et al. Gene transfers from nanoarchaeota to an ancestor of diplomonads and parabasalids. Mol. Biol. Evol. 22 (2005) 85-90
29. Palmer J.D. The symbiotic birth and spread of plastids: how many times and whodunit?. J. Phycol. 39 (2003) 4-11
30. Andersson J.O., et al. Phylogenetic analyses of diplomonad genes reveal frequent lateral gene transfers affecting eukaryotes. Curr. Biol. 13 (2003) 94-104
31. Mitreva M., et al. Comparative genomics of nematodes. Trends Genet. 21 (2005) 573-581
32. Sugimoto-Shirasu K., et al. DNA topoisomerase VI is essential for endoreduplication in Arabidopsis. Curr. Biol. 12 (2002) 1782-1786
33. Hartung F., et al. An archaebacterial topoisomerase homolog not present in other eukaryotes is indispensable for cell proliferation of plants. Curr. Biol. 12 (2002) 1787-1791
34. Sugimoto-Shirasu K., and Roberts K. Big it up: endoreduplication and cell-size control in plants. Curr. Opin. Plant Biol. 6 (2003) 544-553
35. Stebbins G.L. Variation and Evolution in Plants (1950), Columbia Univ. Press
36. Adams K.L., and Wendel J.F. Polyploidy and genome evolution in plants. Curr. Opin. Plant Biol. 8 (2005) 135-141
37. Kurland C.G., et al. Horizontal gene transfer: a critical review. Proc. Natl. Acad. Sci. U. S. A. 100 (2003) 9658-9662
38. Andersson J.O., and Andersson S.G. Insights into the evolutionary process of genome degradation. Curr. Opin. Genet. Dev. 9 (1999) 664-671
39. Wolf Y.I., et al. Evolution of aminoacyl-tRNA synthetases - analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events. Genome Res. 9 (1999) 689-710
40. Gogarten J.P., and Townsend J.P. Horizontal gene transfer, genome innovation and evolution. Nat. Rev. Microbiol. 3 (2005) 679-687
41. Snel B., et al. Genomes in flux: the evolution of archaeal and proteobacterial gene content. Genome Res. 12 (2002) 17-25
42. Hennig W. Phylogenetic Systematics (1966), Univ. Illinois Press
43. Martin W., et al. Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus. Proc. Natl. Acad. Sci. U. S. A. 99 (2002) 12246-12251
44. Esser C., et al. A genome phylogeny for mitochondria among alpha-proteobacteria and a predominantly eubacterial ancestry of yeast nuclear genes. Mol. Biol. Evol. 21 (2004) 1643-1660
45. Rokas A., and Holland P.W. Rare genomic changes as a tool for phylogenetics. Trends Ecol. Evol. 15 (2000) 454-459
46. Archibald J.M., et al. Lateral gene transfer and the evolution of plastid-targeted proteins in the secondary plastid-containing alga Bigelowiella natans. Proc. Natl. Acad. Sci. U. S. A. 100 (2003) 7678-7683
47. Huang J., et al. A first glimpse into the pattern and scale of gene transfer in Apicomplexa. Int. J. Parasitol. 34 (2004) 265-274
48. Kaiser D. Building a multicellular organism. Annu. Rev. Genet. 35 (2001) 103-123
49. Lemieux C., et al. Ancestral chloroplast genome in Mesostigma viride reveals an early branch of green plant evolution. Nature 403 (2000) 649-652
50. Sicheritz-Ponten T., and Andersson S.G. A phylogenomic approach to microbial evolution. Nucleic Acids Res. 29 (2001) 545-552
51. Frickey T., and Lupas A.N. PhyloGenie: automated phylome generation and analysis. Nucleic Acids Res. 32 (2004) 5231-5238
52. th edn (1992), Worth Publishers
53. Morden C.W., and Golden S.S. PsbA genes indicate common ancestry of prochlorophytes and chloroplasts. Nature 337 (1989) 382-385
54. McFadden G.I., and van Dooren G.G. Red algal genome affirms a common origin of all plastids. Curr. Biol. 14 (2004) R514-R516
55. Moreira D., et al. The origin of red algae and the evolution of chloroplasts. Nature 405 (2000) 69-72
56. Rodriguez-Ezpeleta N., et al. Monophyly of primary photosynthetic eukaryotes: green plants, red algae, and glaucophytes. Curr. Biol. 15 (2005) 1325-1330
57. Stiller J.W., et al. Are red algae plants? A critical evaluation of three key molecular data sets. J. Mol. Evol. 52 (2001) 527-539
58. Nozaki H., et al. The phylogenetic position of red algae revealed by multiple nuclear genes from mitochondria-containing eukaryotes and an alternative hypothesis on the origin of plastids. J. Mol. Evol. 56 (2003) 485-497