The slow road to the eukaryotic genome

BioEssays

Volumn 28, Issue 1, 2006, Pages 57-64

  Lester, Leo ^a   Meade, Andrew ^a   Pagel, Mark ^a  

^a UNIVERSITY OF READING   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARCHAEBACTERIUM; BACTERIAL GENE; BACTERIAL GENOME; EUBACTERIACEAE; EUKARYOTE; GENE STRUCTURE; GENE TRANSFER; GENETIC LINKAGE; MOLECULAR EVOLUTION; NONHUMAN; PHYLOGENY; PROKARYOTIC CELL; REVIEW; SPLICEOSOME;

ANIMALS; EUKARYOTIC CELLS; EVOLUTION, MOLECULAR; GENOME; PHYLOGENY; RECOMBINATION, GENETIC;

ARCHAEA; BACTERIA (MICROORGANISMS); EUBACTERIACEAE; EUKARYOTA; PROKARYOTA;

EID: 33645242505     PISSN: 02659247     EISSN: None     Source Type: Journal    
DOI: 10.1002/bies.20344     Document Type: Review

References (62)

1. Martin W, Embley TM. 2004. Early evolution comes full circle. Nature 431:134-136.
2. Woese CR, Fox GE. 1977. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci USA 74:5088-5090.
3. Brown JR, Doolittle WF. 1995. Root of the universal tree of life based on ancient aminoacyl-tRNA synthetase gene duplications. Proc Natl Acad Sci USA 92:2441-2445.
4. Brown JR, Douady CJ, Italia MJ, Marshall WE, Stanhope MJ. 2001. Universal trees based on large combined protein sequence data sets Nat Genet 28:281-285.
5. Daubin V, Gouy M, Perriere G. 2002. A phylogenomic approach to bacterial phylogeny: evidence of a core of genes sharing a common history. Genome Res 12:1080-1090.
6. Iwabe N, Kuma K, Hasegawa M, Osawa S, Miyata T. 1989. Evolutionary relationship of archaebacteria, eubacteria and eukaryotes inferred from phylogenetic trees of duplicated genes. Proc Natl Acad Sci USA 86: 9355-9359.
7. Gribaldo S, Cammarano P. 1998. The root of the universal tree of life inferred from anciently duplicated genes encoding components of the protein-targeting machinery. J Mol Evol 47:508-516.
8. Ribeiro S, Golding GB. 1998. The mosaic nature of the eukaryotic nucleus. Mol Biol Evol 15:779-788.
9. Rivera MC, Jain R, Moore JE, Lake JA. 1998. Genomic evidence for two functionally distinct gene classes. Proc Natl Acad Sci USA 95:6239-6244.
10. Gupta R. 1997. Protein phylogenies and signature sequences: evolutionary relationships within prokaryotes and between prokaryotes and eukaryotes. Antonie van Leeuwenhoek 72:49-61.
11. Martin W. 1999. Mosaic bacterial chromosomes: a challenge en route to a tree of genomes. BioEssays 21:99-104.
12. Katz LA. 2002. Lateral gene transfers and the evolution of eukaryotes: theories and data, Int J Syst Evol Microbiol 52:1893-1900.
13. Martin W, Müller M. 1998. The hydrogen hypothesis for the first eukaryote. Nature 392:37-41.
14. Lopez-Garcia P, Moreira D. 1999. Metabolic symbiosis at the origin of eukaryotes. Trends Biochem Sci 24:88-93.
15. Margulis L. 1970. Origin of Eukaryotic Cells. New Haven: Yale University Press.
16. Martin W, Herrmann RG. 1998. Gene transfer from organelles to the nucleus: how much, what happens, and why? Plant Physiol 118:9-17.
17. Andersson SGE, Kurland CG. 1999. Origins of mitochondria and hydrogenosomes. Curr Opin Microbiol 2:535-541.
18. Moreira D, Lopez-Garcia P. 1998. Symbiosis between methanogenic archaea and d-proteobacteria as the origin of eukaryotes: the syntrophic hypothesis. J Mol Evol 47:517-530.
19. Esser C, Ahmadinejad N, Wiegand C, Rotte C, Sebastiani F, et al. 2004. A genome phylogeny for mitochondria among a-Proteobacteria and a predominantly eubacterial ancestry of yeast nuclear genes. Mol Biol Evol 21:1643-1660.
20. Doolittle WF. 1998. You are what you eat: a gene transfer ratchet could account for bacterial genes in eukaryotic nuclear genomes. Trends Genet 14:307-311.
21. Karlberg O, Canbäck B, Kurland CG, Andersson GE. 2000. The dual origin of the yeast mitochondrial proteome. Yeast 17:170-187.
22. Bapteste E, Gribaldo S. 2003. The genome reduction hypothesis and the phylogeny of eukaryotes. Trends Genet 19:696-700.
23. Rivera MC, Lake JA. 2004. The ring of life provides evidence for a genome fusion origin of eukaryotes. Nature 431:152-155.
24. Lake JA, Rivera MC. 2004. Deriving the genomic tree of life in the presence of horizontal gene transfer: conditioned reconstruction. Mol Biol Evol 21:681-690.
25. Lawrence J, Hendrickson H. 2003. Lateral gene transfer: when will adolescence end? Mol Microbiol 50:739-749.
26. Brown J. 2001. Genomic and phylogenetic perspectives on the evolution of prokaryotes. Syst Biol 50:497-512.
27. Garcia-Vallvé S, Romeu A, Palau J. 2000. Horizontal gene transfer in Bacterial and Archaeal complete genomes. Genome Res 10:1719-1725.
28. 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 28:33-36.
29. Pagel M, Meade A, Barker D. 2004. Bayesian Estimation of Ancestral Character States on Phylogenies. Syst Biol 53:673-684.
30. Ochman H, Lawrence J, Groisman EA. 2000. Lateral gene transfer and the nature of bacterial innovation. Nature 405:299-304.
31. Pagel M. 1999. The maximum likelihood approach to reconstructing ancestral character states of discrete characters on phylogenies. Syst Biol 48:612-622.
32. Brown JR. 2003. Ancient horizontal gene transfer. Nat Rev Genet 4: 121-132.
33. Doolittle WF. 1999. Phylogenetic classification and the universal tree. Science 284:2124-2128.
34. Javaux EJ, Knoll AH, Walter M. 2003. Recognising and interpreting the fossils of early eukaryotes. Origins Life Evol B 33:75-94.
35. Cavalier-Smith T. 2002. The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa. Int J Syst Evol Micr 52:297-354.
36. Gray MW, Long BF, Cedergren R, Golding GB, Lemieux C, et al. 1998. Genome structure and gene content in protist mitochondrial DNAs. Nucleic Acids Res 26:865-878.
37. Prokisch H, Scharfe C, Camp DG II, Xiao W, David L, et al. 2004. Integrative analysis of the mitochondrial proteome in yeast. PLoS Biol 2:795-804.
38. Sickmann A, Reinders J, Wagner Y, Joppich C, Zahedi R, et al. 2003. The proteome of Saccharomyces cerevisiae mitochondria. Proc Natl Acad Sci USA 100:13207-13212.
39. Gabaldon T, Huynen M. 2004. Shaping the mitochondrial proteome. Biochim Biophys Acta 1659:212-220.
40. Gray MW, Burger G, Lang BF. 2001. The origin and early evolution of mitochondria. Genome Biol 2:1018.1-1018.5.
41. Andersson SGE, Kurland CG. 1998. Reductive evolution of resident genomes. Trends Mircobiol 6:263-268.
42. Cavalier-Smith T. 1987. The origin of eukaryote and archaebacterial cells. Ann N Y Acad Sci 503:17-54.
43. Mayr E. 1998. Two empires or three? Proc Natl Acad Sci USA 95:9720-9723.
44. Doolittle WF. 1998. A paradigm gets shifty. Nature 392:15-16.
45. Darnell JE Jr. 1978. Implications of RNA-RNA splicing in evolution of eukaryotic cells. Science 202:1257-1260.
46. Doolittle RF. 2000. Searching for the common ancestor. Res Microbiol 151:85-89.
47. Horiike T, Hamada K, Miyata D, Shinozawa T. 2004. The origin of eukaryotes is suggested as the symbiosis of Pyrococcus into g-Proteobacteria by phylogenetic tree based on gene content. J Mol Evol 59:606-619.
48. Vellai T, Vida G. 1999. The origin of eukaryotes: the difference between prokaryotic and eukaryotic cells. Proc Roy Soc Lond Ser B 266:1571-1577.
49. Doolittle WF. 1999. Rethinking the origin of eukaryotes. Biol Bull 196:378-380.
50. Embley TM, Hirt RP. 1998. Early branching eukaryotes? Curr Opin Genet Dev 8:624-629.
51. Cavalier-Smith T. 2002. Origins of the machinery of recombination and sex. Heredity 88:125-141.
52. Williams BAP, Hirt RP, Lucocq JM, Embley TM. 2002. A mitochondiral remnant in the microsporidian Trachipleistophora hominis. Nature 418:865-869.
53. Searcy DG, Hixon WG. 1991. Cytoskeletal origins in sulfur-metabolising archaebacteria. BioSyst 25:1-11.
54. Sioud M, Baldacci G, Forterre P, Recondo A. 1987. Antitumour drugs inhibit the growth of halophilic archaea. Eur J Biochem 169: 231-236.
55. Löwe J, van den Ent F, Amos LA. 2004. Molecules of the bacterial cytoskeleton. Annu Rev Biophys Biomol Struct 33:177-198.
56. Ferat J, Michel F. 1993. Group II self-splicing introns in bacteria. Nature 364:358-361.
57. Collins L, Penny D. 2005. Complex spliceosomal organization ancestral to extant eukaryotes. Mol Biol Evol 22:1053-1066.
58. Battistuzzi FU, Feijao A, Hedges SB. 2004. A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land. BMC Evol Biol 4:44.
59. Wolf YI, Rogozin IB, Grishin NV, Koonin EV. 2002. Genome trees and the tree of life. Trends Genet 18:472-479.
60. Gupta R, Griffiths E. 2002. Critical issues in bacterial phylogeny. Theor Popul Biol 61:423-434.
61. Qi J, Wang B, Hao B. 2004. Whole proteome prokaryote phylogeny without sequence alignment: a K-string composition approach. J Mol Evol 58:1-11.
62. Dutilh BE, Huynen M, Bruno WJ, Snel B. 2004. The consistent phylogenetic signal in genome trees revealed by reducing the impact of noise. J Mol Evol 58:527-539.