The eukaryotic tree of life: endosymbiosis takes its TOL

Trends in Ecology and Evolution

Volumn 23, Issue 5, 2008, Pages 268-275

  Lane, Christopher E ^a   Archibald, John M ^a  

^a CANADIAN INSTITUTE FOR ADVANCED RESEARCH   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ENDOSYMBIONT; EUKARYOTE; GENE TRANSFER; GENOMICS; HISTORY; PHOTOSYNTHESIS; TAXONOMY;

ARTICLE; EUKARYOTIC CELL; EVOLUTION; GENOME; PHOTOSYNTHESIS; PHYLOGENY; SYMBIOSIS;

EUKARYOTIC CELLS; EVOLUTION; GENOME; PHOTOSYNTHESIS; PHYLOGENY; SYMBIOSIS;

EUKARYOTA; PROTISTA;

EID: 43049085945     PISSN: 01695347     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tree.2008.02.004     Document Type: Article

References (60)

1. McInerney J.O., et al. The prokaryotic tree of life: past, present...and future?. Trends Ecol. Evol. 23 (2008) 276-281
2. Margulis L., and Schwartz K. Five Kingdoms: An Illustrated Guide to the Phyla of Life on Earth (1988), W.H. Freeman
3. Whittaker R.H. New concepts of kingdoms of organisms. Science 163 (1969) 150-160
4. Embley T.M., and Martin W. Eukaryotic evolution, changes and challenges. Nature 440 (2006) 623-630
5. Simpson A.G., and Roger A.J. The real 'kingdoms' of eukaryotes. Curr. Biol. 14 (2004) R693-R696
6. Keeling P.J., et al. The tree of eukaryotes. Trends Ecol. Evol. 20 (2005) 670-676
7. Wegener Parfrey L., et al. Evaluating support for the current classification of eukaryotic diversity. PLoS Genet. 2 (2006) e220
8. 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
9. Archibald A.M., and Keeling P.J. Recycled plastids: a 'green movement' in eukaryotic evolution. Trends Genet. 18 (2002) 577-584
10. Bhattacharya D., et al. How do endosymbionts become organelles? Understanding early events in plastid evolution. BioEssays 29 (2007) 1239-1246
11. Deschamps P., et al. Metabolic symbiosis and the birth of the plant kingdom. Mol. Biol. Evol. 25 (2008) 536-548
12. Martin W., et al. Gene transfer to the nucleus and the evolution of chloroplasts. Nature 393 (1998) 162-165
13. Stoebe B., and Kowallik K.V. Gene-cluster analysis in chloroplast genomics. Trends Genet. 15 (1999) 344-347
14. Sato N., et al. Mass identification of chloroplast proteins of endosymbiotic origin by phylogenetic profiling based on organism-optimized homologous protein groups. Genome Informat. 16 (2005) 56-68
15. Richly E., and Leister D. An improved prediction of chloroplast proteins reveals diversities and commonalities in the chloroplast proteomes of Arabidopsis and rice. Gene 329 (2004) 11-16
16. Moustafa A., and Bhattacharya D. PhyloSort: a user-friendly phylogenetic sorting tool and its application to estimating the cyanobacterial contribution to algal nuclear genomes. BMC Evol. Biol. (2008). http://www.biomedcentral.com/bmcevolbiol 10.1186/1471-2148-1188-1186
17. Reyes-Prieto A., et al. Cyanobacterial contribution to algal nuclear genomes is primarily limited to plastid functions. Curr. Biol. 16 (2006) 2320-2325
18. Brinkmann H., and Martin W. Higher-plant chloroplast and cystolic 3-phosphoglycerate kinases: a case of endosymbiotic gene replacement. Plant Mol. Biol. 30 (1996) 65-75
19. Cavalier-Smith T. Genomic reduction and evolution of novel genetic membranes and protein-targeting machinery in eukaryote-eukaryote chimaeras (meta-algae). Philos. Trans. R. Soc. Lond. B Biol. Sci. 358 (2003) 109-134
20. Takahashi F., et al. Origins of the secondary plastids of euglenophyta and chlorarachniophyta as revealed by an analysis of the plastid-targeting, nuclear-encoded gene psbO. J. Phycol. 43 (2007) 1302-1309
21. Cavalier-Smith T. The phagotrophic origin of eukaryotes and phylogenetic classification of protozoa. Int. J. Syst. Evol. Micro. 52 (2002) 297-354
22. Rogers M.B., et al. The complete chloroplast genome of the chlorarachniophyte Bigelowiella natans: evidence for independent origins of chlorarachniophyte and euglenid secondary endosymbionts. Mol. Biol. Evol. 24 (2007) 54-62
23. Harper J.T., and Keeling P.J. Nucleus-encoded, plastid-targeted glyceraldehyde-3-phosphate dehydrogenase (GAPDH) indicates a single origin for chromalveolate plastids. Mol. Biol. Evol. 20 (2003) 1730-1735
24. Patron N.J., et al. Gene replacement of fructose-1,6-bisphosphate aldolase supports the hypothesis of a single photosynthetic ancestor of chromalveolates. Eukaryot. Cell 3 (2004) 1169-1175
25. Li S.L., et al. Phylogenomic analysis identifies red algal genes of endosymbiotic origin in the chromalveolates. Mol. Biol. Evol. 23 (2006) 663-674
26. Nosenko T., and Bhattacharya D. Horizontal gene transfer in chromalveolates. BMC Evol. Biol. 7 (2007) 173
27. Armbrust E.V., et al. The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism. Science 306 (2004) 79-86
28. Ahmadinejad N., et al. Genome history in the symbiotic hybrid Euglena gracilis. Gene 402 (2007) 35-39
29. Tyler B.M., et al. Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis. Science 313 (2006) 1261-1266
30. Matsuzaki M., et al. Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D. Nature 428 (2004) 653
31. Yoon H.S., et al. Defining the major lineages of red algae (Rhodophyta). J. Phycol. 42 (2006) 482-492
32. Rodríguez-Ezpeleta N., et al. Detecting and overcoming systematic errors in genome-scale phylogenies. Syst. Biol. 56 (2007) 389-399
33. Stibitz T.B., et al. Symbiotic origin of a novel actin gene in the cryptophyte Pyrenomonas helgolandii. Mol. Biol. Evol. 17 (2000) 1731-1738
34. Tanifuji G., et al. Diversity of secondary endosymbiont-derived actin-coding genes in cryptomonads and their evolutionary implications. J. Plant Res. 119 (2006) 205-215
35. Hackett J.D., et al. Phylogenomic analysis supports the monophyly of cryptophytes and haptophytes and the association of Rhizaria with chromalveolates. Mol. Biol. Evol. 24 (2007) 1702-1713
36. Palmer J.D. The symbiotic birth and spread of plastids: how many times and whodunit?. J. Phycol. 39 (2003) 4-11
37. Archibald J.M. Jumping genes and shrinking genomes - probing the evolution of eukaryotic photosynthesis using genomics. IUBMB Life 57 (2005) 539-547
38. Patron N.J., et al. Multiple gene phylogenies support the monophyly of cryptomonad and haptophyte host lineages. Curr. Biol. 17 (2007) 887-891
39. Burki F., et al. Phylogenomics reshuffles the eukaryotic supergroups. PLoS ONE 2 (2007) e790
40. Rice D.W., and Palmer J.D. An exceptional horizontal gene transfer in plastids: gene replacement by a distant bacterial paralog and evidence that haptophyte and cryptophyte plastids are sisters. BMC Biol. 4 (2006) 31
41. Huang J., et al. Phylogenomic evidence supports past endosymbiosis, intracellular and horizontal gene transfer in Cryptosporidium parvum. Genome Biol. 5 (2004) R88
42. Moore R.B., et al. A photosynthetic alveolate closely related to apicomplexans parasites. Nature 451 (2008) 959-963
43. 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
44. Rogers M.B., et al. A complex and punctate distribution of three eukaryotic genes derived by lateral gene transfer. BMC Evol. Biol. 7 (2007) 89
45. Leigh J.W., et al. Testing congruence in phylogenomic analysis. Syst. Biol. 57 (2008) 4-15
46. Nozaki H., and Iseki M. Phylogeny of primary photosynthetic eukaryotes as deduced from slowly evolving nuclear genes. Mol. Biol. Evol. 24 (2007) 1592-1595
47. Yoon H.S., et al. A molecular timeline for the origin of photosynthetic eukaryotes. Mol. Biol. Evol. 21 (2004) 809-818
48. Larkum A.W.D., et al. Shopping for plastids. Trends Plant Sci. 12 (2007) 189-195
49. Stiller J.W. Plastid endosymbiosis, genome evolution and the origin of green plants. Trends Plant Sci. 12 (2007) 391-396
50. Stiller J.W., et al. A single origin of plastids revisited: convergent evolution in organellar genome content. J. Phycol. 39 (2003) 95-105
51. Cavalier-Smith T. Principles of protein and lipid targeting in secondary symbiogenesis: euglenoid, dinoflagellate, and sporozoan plastid origins and the eukaryote family tree. J. Eukaryot. Microbiol. 46 (1999) 347-366
52. Archibald J.M. Nucleomorph genomes: structure, function, origin and evolution. BioEssays 29 (2007) 1239-1246
53. Yoon H.S., et al. Tertiary endosymbiosis driven genome evolution in dinoflagellate algae. Mol. Biol. Evol. 22 (2005) 1299-1308
54. Rodríguez-Ezpeleta N., et al. Toward resolving the eukaryotic tree: the phylogenetic positions of jakobids and cercozoans. Curr. Biol. 17 (2007) 1420-1425
55. Bodyl A. Do plastid-related characters support the chromalveolate hypothesis?. J. Phycol. 41 (2005) 712-719
56. Bodyl A., and Moszczynski K. Did the peridinin plastid evolve through tertiary endosymbiosis? A hypothesis. Eur. J. Phycol. 41 (2006) 435-448
57. Bodyl A., et al. The intracellular cyanobacteria of Paulinelia chromatophora: endosymbionts or organelles?. Trends Microbiol. 15 (2007) 295-296
58. Huang J., et al. A first glimpse into the pattern and scale of gene transfer in Apicomplexa. Int. J. Parasitol. 34 (2004) 265-274
59. Teles-Grilo M.L., et al. Is there a plastid in Perkinsus atlanticus (Phylum Perkinsozoa)?. Eur. J. Protistol. 43 (2007) 163-167
60. Frickey T., and Lupas A.N. PhyloGenie: automated phylome generation and analysis. Nucleic Acids Res. 32 (2004) 5231-5238