Gene transfer and diversification of microbial eukaryotes

Annual Review of Microbiology

Volumn 63, Issue , 2009, Pages 177-193

  Andersson, Jan O ^a  

^a UPPSALA UNIVERSITY   (Sweden)

Author keywords

Adaptation; Algae; Comparative genomics; Gene acquisition; Horizontal gene transfer; Protist

Indexed keywords

ACANTHAMOEBA; ADAPTATION; ALGA; ALPHAPROTEOBACTERIA; ASCOMYCETES; ASCOVIRUS; BACTERIOPHAGE; BACTEROIDES; BACULOVIRUS; CYANOBACTERIUM; ECOLOGICAL NICHE; EPSILONPROTEOBACTERIA; EUKARYOTE; EUKARYOTE EVOLUTION; FIRMICUTES; FUSOBACTERIA; GENE TRANSFER; GENETIC LINE; GENETIC VARIABILITY; MICROBIAL METABOLISM; NONHUMAN; PHAGOTROPH; PRIORITY JOURNAL; PROKARYOTE; REVIEW; SOIL MICROFLORA; VIRUS INFECTION;

BIODIVERSITY; CLUSTER ANALYSIS; EUKARYOTIC CELLS; EVOLUTION, MOLECULAR; GENE TRANSFER, HORIZONTAL; PHYLOGENY;

ALGAE; EUKARYOTA; PROKARYOTA; PROTISTA;

EID: 70049087749     PISSN: 00664227     EISSN: None     Source Type: Book Series    
DOI: 10.1146/annurev.micro.091208.073203     Document Type: Review

References (86)

1. Abby S, Daubin V. 2007. Comparative genomics and the evolution of prokaryotes. Trends Microbiol. 15:135-141
2. Adl SM, Simpson AG, Farmer MA, Andersen RA, Anderson OR, et al. 2005. The new higher level classification of eukaryotes with emphasis on the taxonomy of protists. J. Eukaryot. Microbiol. 52:399-451
3. Andersson JO. 2000. Evolutionary genomics: Is Buchnera a bacterium or an organelle? Curr. Biol. 10:R866-R68
4. Andersson JO. 2005. Lateral gene transfer in eukaryotes. Cell. Mol. Life Sci. 62:1182-1197
5. Andersson JO. 2006. Genome evolution of anaerobic protists: metabolic adaptation via gene acquisition. In Genomics and Evolution of Microbial Eukaryotes, ed. LA Katz, D Bhattacharya, pp. 109-122 Oxford: Oxford Univ. Press
6. Andersson JO, Hirt RP, Foster PG, Roger AJ. 2006. Evolution of four gene families with patchy phylogenetic distribution: influx of genes into protist genomes. BMC Evol. Biol. 6:27
7. Andersson JO, Sjögren ÅM, Davis LAM, Embley TM, Roger AJ. 2003. Phylogenetic analyses of diplomonad genes reveal frequent lateral gene transfers affecting eukaryotes. Curr. Biol. 13:94-104 (Pubitemid 36154336)
8. Andersson JO, Sjögren ÅM, Horner DS, Murphy CA, Dyal PL, et al. 2007. A genomic survey of the fish parasite Spironucleus salmonicida indicates genomic plasticity among diplomonads and significant lateral gene transfer in eukaryote genome evolution. BMC Genomics 8:51 (Pubitemid 46358509)
9. Annoura T, Sariego I, Nara T, Makiuchi T, Fujimura T, et al. 2007. Dihydroorotate dehydrogenase arises from novel fused gene product with aspartate carbamoyltransferase in Bodo saliens. Biochem. Biophys. Res. Commun. 358:253-258 (Pubitemid 46719111)
10. Armbrust EV, Berges JA, Bowler C, Green BR, Martinez D, et al. 2004. The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism. Science 306:79-86 (Pubitemid 39451941)
11. Becker B, Hoef-Emden K, Melkonian M. 2008. Chlamydial genes shed light on the evolution of photoautotrophic eukaryotes. BMC Evol. Biol. 8:203
12. Belbahri L, Calmin G, Mauch F, Andersson JO. 2008. Evolution of the cutinase gene family: evidence for lateral gene transfer of a candidate Phytophthora virulence factor. Gene 408:1-8
13. Bhattacharya D, Yoon HS, Hackett JD. 2004. Photosynthetic eukaryotes unite: Endosymbiosis connects the dots. BioEssays 26:50-60 (Pubitemid 38095348)
14. Bowler C, Allen AE, Badger JH, Grimwood J, Jabbari K, et al. 2008. The Phaeodactylum genome reveals the evolutionary history of diatom genomes. Nature 456:239-244
15. Carlton JM, Hirt RP, Silva JC, Delcher AL, Schatz M, et al. 2007. Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis. Science 315:207-212 (Pubitemid 46166360)
16. Craig JP, Bekal S, Hudson M, Domier L, Niblack T, Lambert KN. 2008. Analysis of a horizontally transferred pathway involved in vitamin B6 biosynthesis from the soybean cyst nematode Heterodera glycines. Mol. Biol. Evol. 25:2085-2098
17. Dao DN, Kessin RH, Ennis HL. 2000. Developmental cheating and the evolutionary biology of Dictyostelium and Myxococcus. Microbiology 146:1505-1512 (Pubitemid 30458705)
18. De Jonckheere JF. 2002. A century of research on the amoeboflagellate genus Naegleria. Acta Protozool. 41:309-342
19. Denker E, Bapteste E, Le Guyader H, Manuel M, Rabet N. 2008. Horizontal gene transfer and the evolution of cnidarian stinging cells. Curr. Biol. 18:R858-59
20. Deusch O, Landan G, Roettger M, Gruenheit N, Kowallik KV, et al. 2008. Genes of cyanobacterial origin in plant nuclear genomes point to a heterocyst-forming plastid ancestor. Mol. Biol. Evol. 25:748-761
21. 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
22. Eichinger L, Pachebat JA, Glöckner G, Rajandream MA, Sucgang R, et al. 2005. The genome of the social amoeba Dictyostelium discoideum. Nature 435:43-57 (Pubitemid 40655903)
23. Embley TM. 2006. Multiple secondary origins of the anaerobic lifestyle in eukaryotes. Philos. Trans. R. Soc. London B Biol. Sci. 361:1055-1067
24. Embley TM, Martin W. 2006. Eukaryotic evolution, changes and challenges. Nature 440:623-630
25. Emiliani G, Fondi M, Fani R, Gribaldo S. 2009. A horizontal gene transfer at the origin of phenylpropanoid metabolism: a key adaptation of plants to land. Biol. Direct 4:7
26. Feschotte C, Pritham EJ. 2007. DNA transposons and the evolution of eukaryotic genomes. Annu. Rev. Genet. 41:331-368
27. Filée J, Pouget N, Chandler M. 2008. Phylogenetic evidence for extensive lateral acquisition of cellular genes by nucleocytoplasmic large DNA viruses. BMC Evol. Biol. 8:320
28. Filée J, Siguier P, Chandler M. 2007. I am what I eat and I eat what I am: acquisition of bacterial genes by giant viruses. Trends Genet. 23:10-15 (Pubitemid 44960530)
29. Fitzpatrick DA, Logue ME, Butler G. 2008. Evidence of recent interkingdom horizontal gene transfer between bacteria and Candida parapsilosis. BMC Evol. Biol. 8:181 (Pubitemid 351999911)
30. Friesen TL, Stukenbrock EH, Liu Z, Meinhardt S, Ling H, et al. 2006. Emergence of a new disease as a result of interspecific virulence gene transfer. Nat. Genet. 38:953-956 (Pubitemid 44141666)
31. Garcia-Vallvé S, Romeu A, Palau J. 2000. Horizontal gene transfer of glycosyl hydrolases of the rumen fungi. Mol. Biol. Evol. 17:352-361 (Pubitemid 30123756)
32. Genereux DP, Logsdon JM Jr. 2003. Much ado about bacteria-to-vertebrate lateral gene transfer. Trends Genet. 19:191-195 (Pubitemid 36398420)
33. Gladyshev EA, Meselson M, Arkhipova IR. 2008. Massive horizontal gene transfer in bdelloid rotifers. Science 320:1210-1213 (Pubitemid 351929508)
34. Gogarten JP. 2003. Gene transfer: gene swapping craze reaches eukaryotes. Curr. Biol. 13:R53-54
35. Gojković Z, Knecht W, Zameitat E, Warneboldt J, Coutelis JB, et al. 2004. Horizontal gene transfer promoted evolution of the ability to propagate under anaerobic conditions in yeasts. Mol. Genet. Genomics 271:387-393 (Pubitemid 38824032)
36. Hall C, Brachat S, Dietrich FS. 2005. Contribution of horizontal gene transfer to the evolution of Saccharomyces cerevisiae. Eukaryot. Cell 4:1102-1115 (Pubitemid 40817469)
37. Hall C, Dietrich FS. 2007. The reacquisition of biotin prototrophy in Saccharomyces cerevisiae involved horizontal gene transfer, gene duplication and gene clustering. Genetics 177:2293-2307 (Pubitemid 350277006)
38. Hotopp JC, Clark ME, Oliveira DC, Foster JM, Fischer P, et al. 2007. Widespread lateral gene transfer from intracellular bacteria to multicellular eukaryotes. Science 317:1753-1756 (Pubitemid 47461840)
39. Huang J, Gogarten JP. 2007. Did an ancient chlamydial endosymbiosis facilitate the establishment of primary plastids? Genome Biol. 8:R99 (Pubitemid 351903180)
40. Huang J, Gogarten JP. 2008. Concerted gene recruitment in early plant evolution. Genome Biol. 9:R109
41. Huang J, Mullapudi N, Lancto CA, Scott M, Abrahamsen MS, Kissinger JC. 2004. Phylogenomic evidence supports past endosymbiosis, intracellular and horizontal gene transfer in Cryptosporidium parvum. Genome Biol. 5:R88
42. Inderbitzin P, Harkness J, Turgeon BG, Berbee ML. 2005. Lateral transfer of mating system in Stemphylium. Proc. Natl. Acad. Sci. USA 102:11390-11395 (Pubitemid 41153830)
43. Jain R, Yuen IS, Taphouse CR, Gomer RH. 1992. A density-sensing factor controls development in Dictyostelium. Genes Dev. 6:390-400
44. Keeling PJ, Palmer JD. 2008. Horizontal gene transfer in eukaryotic evolution. Nat. Rev. Genet. 9:605-618
45. Kenrick P, Crane PR. 1997. The origin and early evolution of plants on land. Nature 389:33-39 (Pubitemid 27387682)
46. Khaldi N, Collemare J, Lebrun MH, Wolfe KH. 2008. Evidence for horizontal transfer of a secondary metabolite gene cluster between fungi. Genome Biol. 9:R18 (Pubitemid 351911929)
47. Kidwell MG. 1993. Lateral transfer in natural populations of eukaryotes. Annu. Rev. Genet. 27:235-256 (Pubitemid 24011354)
48. Kolattukudy PE, Rogers LM, Li D, Hwang CS, Flaishman MA. 1995. Surface signaling in pathogenesis. Proc. Natl. Acad. Sci. USA 92:4080-4087
49. Kumar S, Hedges SB. 1998. A molecular timescale for vertebrate evolution. Nature 392:917-920
50. Lane CE, Archibald JM. 2008. The eukaryotic tree of life: Endosymbiosis takes its TOL. Trends Ecol. Evol. 23:268-275
51. Latijnhouwers M, de Wit PJ, Govers F. 2003. Oomycetes and fungi: similar weaponry to attack plants. Trends Microbiol. 11:462-469 (Pubitemid 37214873)
52. Lawrence JG. 2005. Common themes in the genome strategies of pathogens. Curr. Opin. Genet. Dev. 15:584-588
53. Loftus B, Anderson I, Davies R, Alsmark UCM, Samuelson J, et al. 2005. The genome of the protist parasite Entamoeba histolytica. Nature 433:865-868 (Pubitemid 40314894)
54. Marin B, Nowack EC, Melkonian M. 2005. A plastid in the making: evidence for a second primary endosymbiosis. Protist 156:425-432 (Pubitemid 41682020)
55. Martens C, Vandepoele K, Van de Peer Y. 2008. Whole-genome analysis reveals molecular innovations and evolutionary transitions in chromalveolate species. Proc. Natl. Acad. Sci. USA 105:3427-3432 (Pubitemid 351723569)
56. Moreira D, Brochier-Armanet C. 2008. Giant viruses, giant chimeras: the multiple evolutionary histories of Mimivirus genes. BMC Evol. Biol. 8:12 (Pubitemid 351342674)
57. Morrison HG, McArthur AG, Gillin FD, Aley SB, Adam RD, et al. 2007. Genomic minimalism in the early diverging intestinal parasite Giardia lamblia. Science 317:1921-1926
58. Nedelcu AM, Miles IH, Fagir AM, Karol K. 2008. Adaptive eukaryote-to-eukaryote lateral gene transfer: stress-related genes of algal origin in the closest unicellular relatives of animals. J. Evol. Biol. 21:1852-1860
59. Nikoh N, Nakabachi A. 2009. Aphids acquired symbiotic genes via lateral gene transfer. BMC Biol. 7:12
60. Nosenko T, Bhattacharya D. 2007. Horizontal gene transfer in chromalveolates. BMC Evol. Biol. 7:173
61. Nowack EC, Melkonian M, Glockner G. 2008. Chromatophore genome sequence of Paulinella sheds light on acquisition of photosynthesis by eukaryotes. Curr. Biol. 18:410-418
62. Oliver RP, Solomon PS. 2008. Recent fungal diseases of crop plants: Is lateral gene transfer a common theme? Mol. Plant-Microbe Interact. 21:287-293
63. Opperdoes FR, Michels PA. 2007. Horizontal gene transfer in trypanosomatids. Trends Parasitol. 23:470-476
64. Pace JK 2nd, Gilbert C, Clark MS, Feschotte C. 2008. Repeated horizontal transfer of a DNA transposon in mammals and other tetrapods. Proc. Natl. Acad. Sci. USA 105:17023-17028
65. Parfrey LW, Barbero E, Lasser E, Dunthorn M, Bhattacharya D, et al. 2006. Evaluating support for the current classification of eukaryotic diversity. PLoS Genet 2:e220 (Pubitemid 46045187)
66. Patron NJ, Waller RF, Cozijnsen AJ, Straney DC, Gardiner DM, et al. 2007. Origin and distribution of epipolythiodioxopiperazine (ETP) gene clusters in filamentous ascomycetes. BMC Evol. Biol. 7:174
67. Peacock CS, Seeger K, Harris D, Murphy L, Ruiz JC, et al. 2007. Comparative genomic analysis of three Leishmania species that cause diverse human disease. Nat. Genet. 39:839-847 (Pubitemid 47014491)
68. Reyes-Prieto A, Hackett JD, Soares MB, Bonaldo MF, Bhattacharya D. 2006. Cyanobacterial contribution to algal nuclear genomes is primarily limited to plastid functions. Curr. Biol. 16:2320-2325 (Pubitemid 44821835)
69. Ricard G, McEwan NR, Dutilh BE, Jouany JP, Macheboeuf D, et al. 2006. Horizontal gene transfer from bacteria to rumen ciliates indicates adaptation to their anaerobic carbohydrates rich environment. BMC Genomics 7:22
70. Richards TA, Dacks JB, Jenkinson JM, Thornton CR, Talbot NJ. 2006. Evolution of filamentous plant pathogens: gene exchange across eukaryotic kingdoms. Curr. Biol. 16:1857-1864 (Pubitemid 44354141)
71. Rogers MB, Watkins RF, Harper JT, Durnford DG, Gray MW, Keeling PJ. 2007. A complex and punctate distribution of three eukaryotic genes derived by lateral gene transfer. BMC Evol. Biol. 7:89
72. Rumpho ME, Worful JM, Lee J, Kannan K, Tyler MS, et al. 2008. Horizontal gene transfer of the algal nuclear gene psbO to the photosynthetic sea slug Elysia chlorotica. Proc. Natl. Acad. Sci. USA 105:17867-17871
73. Sanderson MJ, Thorne JL, Wikstrom N, Bremer K. 2004. Molecular evidence on plant divergence times. Am. J. Bot. 91:1656-1665 (Pubitemid 43193724)
74. Schmitz-Esser S, Haferkamp I, Knab S, Penz T, Ast M, et al. 2008. Lawsonia intracellularis contains a gene encoding a functional rickettsia-like ATP/ADP translocase for host exploitation. J. Bacteriol. 190:5746-5752
75. Shi NQ, Jeffries TW. 1998. Anaerobic growth and improved fermentation of Pichia stipitis bearing a URA1 gene from Saccharomyces cerevisiae. Appl. Microbiol. Biotechnol. 50:339-345
76. Simpson AGB, Perley TA, Lara E. 2008. Lateral transfer of the gene for a widely used marker, alpha-tubulin, indicated by a multi-protein study of the phylogenetic position of Andalucia (Excavata). Mol. Phylogenet. Evol. 47:366-377
77. Slot JC, Hibbett DS. 2007. Horizontal transfer of a nitrate assimilation gene cluster and ecological transitions in fungi: a phylogenetic study. PLoS ONE 2:e1097
78. Smith MW, Feng DF, Doolittle RF. 1992. Evolution by acquisition: the case for horizontal gene transfers. Trends Biochem. Sci. 17:489-493
79. Stukenbrock EH, McDonald BA. 2008. The origins of plant pathogens in agro-ecosystems. Annu. Rev. Phytopathol. 46:75-100
80. Sugimoto-Shirasu K, Stacey NJ, Corsar J, Roberts K, McCann MC. 2002. DNA topoisomerase VI is essential for endoreduplication in Arabidopsis. Curr. Biol. 12:1782-1786 (Pubitemid 35169796)
81. Temporini ED, VanEtten HD. 2002. Distribution of the pea pathogenicity (PEP) genes in the fungus Nectria haematococca mating population VI. Curr. Genet. 41:107-114
82. Temporini ED, VanEtten HD. 2004. An analysis of the phylogenetic distribution of the pea pathogenicity genes of Nectria haematococca MPVI supports the hypothesis of their origin by horizontal transfer and uncovers a potentially new pathogen of garden pea: Neocosmospora boniensis. Curr. Genet. 46:29-36
83. Timmis JN, Ayliffe MA, Huang CY, Martin W. 2004. Endosymbiotic gene transfer: Organelle genomes forge eukaryotic chromosomes. Nat. Rev. Genet. 5:123-135 (Pubitemid 38160279)
84. Tomas A, Feng GH, Reeck GR, Bockus WW, Leach JE. 1990. Purification of a cultivar-specific toxin from Pyrenophora tritici-repentis, causal agent of tan spot of wheat. Mol. Plant-Microbe Interact. 3:221-224
85. Wenzl P, Wong L, Kwang-Won K, Jefferson RA. 2005. A functional screen identifies lateral transfer of β-glucuronidase (gus) from bacteria to fungi. Mol. Biol. Evol. 22:308-316 (Pubitemid 40130198)
86. Zhang JZ. 2003. Evolution by gene duplication: an update. Trends Ecol. Evol. 18:292-298