Gene repertoire of amoeba-associated giant viruses

Intervirology

Volumn 53, Issue 5, 2010, Pages 330-343

  Colson, Philippe ^a,b   Raoult, Didier ^a,b  

^a CNRS   (France)

^b TIMONE HOSPITAL   (France)

Author keywords

Acanthamoeba polyphaga mimivirus; Core genes; Gene duplication; Giant virus; Lateral gene transfer; Marseillevirus; Mimiviridae; Nucleo cytoplasmic large DNA viruses; Virophage

Indexed keywords

AMOEBA (GENUS); DNA VIRUS; EUKARYOTE; GENE DUPLICATION; GENOME SIZE; GIANT VIRUS; HORIZONTAL GENE TRANSFER; MARSEILLEVIRUS; MIMIVIRUS; NONHUMAN; NUCLEOCYTOPLASMIC LARGE DNA VIRUS; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; ORGANISM GROUP SIZE; PRIORITY JOURNAL; REVIEW; SEQUENCE HOMOLOGY; SPUTNIK VIROPHAGE; SYMPATRY; VIRAL GENETICS; VIRUS; VIRUS GENE; VIRUS GENOME; VIRUS ISOLATION;

AMOEBA; ARCHAEA; BACTERIA; DNA VIRUSES; EUKARYOTA; EVOLUTION, MOLECULAR; GENE TRANSFER, HORIZONTAL; GENES, VIRAL; GENOME, VIRAL; OPEN READING FRAMES; RECOMBINATION, GENETIC; SEQUENCE HOMOLOGY; VIRAL PROTEINS;

ACANTHAMOEBA POLYPHAGA MIMIVIRUS; AMOEBA (GENUS); DNA VIRUSES; EUKARYOTA; MIMIVIRUS;

EID: 77953710766     PISSN: 03005526     EISSN: None     Source Type: Journal    
DOI: 10.1159/000312918     Document Type: Review

References (113)

1. Fuhrman JA: Marine viruses and their biogeochemical and ecological effects. Nature 1999; 399: 541-548.
2. Suttle CA: Viruses in the sea. Nature 2005; 437: 356-361.
3. Woese C: The universal ancestor. Proc Natl Acad Sci USA 1998; 95: 6854-6859.
4. Woese CR, Kandler O, Wheelis ML: Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 1990; 87: 4576-4579.
5. van Regenmortel MHV: 7th report of the International Committee on taxonomy of Viruses. San Diego, Academic Press, 2000, pp 3-16.
6. Lwoff A: The concept of virus. J Gen Microbiol 1957; 17: 239-253.
7. Raoult D, La Scola B, Birtles R: The discovery and characterization of Mimivirus, the largest known virus and putative pneumonia agent. Clin Infect Dis 2007; 45: 95-102.
8. La Scola B, Desnues C, Pagnier I, Robert C, Barrassi L, Fournous G, Merchat M, Suzan- Monti M, Forterre P, Koonin E, Raoult D: The virophage as a unique parasite of the giant mimivirus. Nature 2008; 455: 100-104.
9. Raoult D, Audic S, Robert C, Abergel C, Renesto P, Ogata H, La Scola B, Suzan M, Claverie JM: The 1.2-megabase genome sequence of Mimivirus. Science 2004; 306: 1344-1350.
10. La Scola B, Audic S, Robert C, Jungang L, de Lamballerie X, Drancourt M, Birtles R, Claverie JM, Raoult D: A giant virus in amoebae. Science 2003; 299: 2033.
11. Boyer L, Yutin N, Pagnier I, Barassi L, Fournous G, Espinosa L, Robert C, Azza S, Sun S, Rossmann MG, Suzan-Monti M, La Scola B, Koonin EV, Raoult D: Giant Marseillevirus highlights the role of amoebae as a melting pot in emergence of chimeric microorganisms. Proc Natl Acad Sci USA 2009; 106: 21848-21853.
12. Iyer LM, Balaji S, Koonin EV, Aravind L: Evolutionary genomics of nucleo-cytoplasmic large DNA viruses. Virus Res 2006; 117: 156-184.
13. Koonin EV: Virology: Gulliver among the Lilliputians. Curr Biol 2005; 15:R167-R169.
14. Claverie JM, Abergel C: Mimivirus and its virophage. Annu Rev Genet 2009; 43: 49-66.
15. Yamada T, Onimatsu H, Van Etten JL: Chlorella viruses. Adv Virus Res 2006; 66: 293-336.
16. Delaroque N, Boland W, Muller DG, Knippers R: Comparisons of two large phaeoviral genomes and evolutionary implications. J Mol Evol 2003; 57: 613-622.
17. Freeman MJ, Plasterer NT, Smith FT, Mohr CS: Patterns of genome organization in bacteria. Science 1998; 279: 1827.
18. Galperin MY, Koonin EV: 'Conserved hypothetical' proteins: prioritization of targets for experimental study. Nucleic Acids Res 2004; 32: 5452-5463.
19. Koonin EV: Orthologs, paralogs, and evolutionary genomics. Annu Rev Genet 2005; 39: 309-338.
20. Fitzgerald LA, Graves MV, Li X, Feldblyum T, Nierman WC, Van Etten JL: Sequence and annotation of the 369-kb NY-2A and the 345-kb AR158 viruses that infect Chlorella NC64A. Virology 2007; 358: 472-484. (Pubitemid 46157034)
21. Byrne D, Grzela R, Lartigue A, Audic S, Chenivesse S, Encinas S, Claverie JM, Abergel C: The polyadenylation site of Mimivirus transcripts obeys a stringent 'hairpin rule'. Genome Res 2009; 19: 1233-1242.
22. Suhre K, Audic S, Claverie JM: Mimivirus gene promoters exhibit an unprecedented conservation among all eukaryotes. Proc Natl Acad Sci USA 2005; 102: 14689-14693.
23. Wilson WH, Schroeder DC, Allen MJ, Holden MT, Parkhill J, Barrell BG, Churcher C, Hamlin N, Mungall K, Norbertczak H, Quail MA, Price C, Rabbinowitsch E, Walker D, Craigon M, Roy D, Ghazal P: Complete genome sequence and lytic phase transcription profile of a Coccolithovirus. Science 2005; 309: 1090-1092.
24. Hutson MS, Duke T, Viovy JL: Two-dimensional motion of DNA bands during 120° pulsed-field gel electrophoresis. I. Effect of molecular weight. Biopolymers 1995; 35: 297-306.
25. Claverie JM, Ogata H, Audic S, Abergel C, Suhre K, Fournier PE: Mimivirus and the emerging concept of 'giant' virus. Virus Res 2006; 117: 133-144.
26. Koonin EV, Senkevich TG, Dolja VV: The ancient Virus World and evolution of cells. Biol Direct 2006; 1: 29.
27. Iyer LM, Aravind L, Koonin EV: Common origin of four diverse families of large eukaryotic DNA viruses. J Virol 2001; 75: 11720-11734.
28. Yutin N, Wolf YI, Raoult D, Koonin EV: Eukaryotic large nucleo-cytoplasmic DNA viruses: clusters of orthologous genes and reconstruction of viral genome evolution. Virol J 2009; 6: 223.
29. Awadalla P: The evolutionary genomics of pathogen recombination. Nat Rev Genet 2003; 4: 50-60.
30. Moreira D, Lopez-Garcia P: Ten reasons to exclude viruses from the tree of life. Nat Rev Microbiol 2009; 7: 306-311.
31. Moreira D, Brochier-Armanet C: Giant viruses, giant chimeras: The multiple evolutionary histories of Mimivirus genes. BMC Evol Biol 2008; 8: 12.
32. Moreira D, Lopez-Garcia P: Comment on 'The 1.2-megabase genome sequence of Mimivirus'. Science 2005; 308: 1114.
33. Andersson JO: Lateral gene transfer in eukaryotes. Cell Mol Life Sci 2005; 62: 1182-1197.
34. Lawrence JG, Ochman H: Amelioration of bacterial genomes: rates of change and exchange. J Mol Evol 1997; 44: 383-397.
35. Jain R, Rivera MC, Moore JE, Lake JA: Horizontal gene transfer accelerates genome innovation and evolution. Mol Biol Evol 2003; 20: 1598-1602.
36. Canchaya C, Fournous G, Chibani-Chennoufi S, Dillmann ML, Brussow H: Phage as agents of lateral gene transfer. Curr Opin Microbiol 2003; 6: 417-424.
37. Filee J, Bapteste E, Susko E, Krisch HM: A selective barrier to horizontal gene transfer in the T4-type bacteriophages that has preserved a core genome with the viral replication and structural genes. Mol Biol Evol 2006; 23: 1688-1696.
38. Filee J, Tetart F, Suttle CA, Krisch HM: Marine T4-type bacteriophages, a ubiquitous component of the dark matter of the biosphere. Proc Natl Acad Sci USA 2005; 102: 12471-12476.
39. Lindell D, Sullivan MB, Johnson ZI, Tolonen AC, Rohwer F, Chisholm SW: Transfer of photosynthesis genes to and from Prochlorococcus viruses. Proc Natl Acad Sci USA 2004; 101: 11013-11018.
40. Millard A, Clokie MR, Shub DA, Mann NH: Genetic organization of the psbAD region in phages infecting marine Synechococcus strains. Proc Natl Acad Sci USA 2004; 101: 11007-11012.
41. McGeoch DJ, Rixon FJ, Davison AJ: Topics in herpesvirus genomics and evolution. Virus Res 2006; 117: 90-104.
42. Alcami A, Koszinowski UH: Viral mechanisms of immune evasion. Trends Microbiol 2000; 8: 410-418.
43. McFadden G, Murphy PM: Host-related immunomodulators encoded by poxviruses and herpesviruses. Curr Opin Microbiol 2000; 3: 371-378.
44. Moore PS, Boshoff C, Weiss RA, Chang Y: Molecular mimicry of human cytokine and cytokine response pathway genes by KSHV. Science 1996; 274: 1739-1744.
45. Fu M, Deng R, Wang J, Wang X: Detection and analysis of horizontal gene transfer in herpesvirus. Virus Res 2008; 131: 65-76.
46. Filee J, Pouget N, Chandler M: Phylogenetic evidence for extensive lateral acquisition of cellular genes by nucleocytoplasmic large DNA viruses. BMC Evol Biol 2008; 8: 320.
47. Esposito JJ, Sammons SA, Frace AM, Osborne JD, Olsen-Rasmussen M, Zhang M, Govil D, Damon IK, Kline R, Laker M, Li Y, Smith GL, Meyer H, Leduc JW, Wohlhueter RM: Genome sequence diversity and clues to the evolution of variola (smallpox) virus. Science 2006; 313: 807-812.
48. Filee J: Lateral gene transfer, lineage-specific gene expansion and the evolution of Nucleo Cytoplasmic Large DNA viruses. J Invertebr Pathol 2009; 101: 169-171.
49. Ogata H, Abergel C, Raoult D, Claverie JM: Response to Comment on 'The 1.2-Megabase genome sequence of Mimivirus'. Science 2005; 308: 1114b.
50. Suzan-Monti M, La Scola B, Raoult D: Genomic and evolutionary aspects of Mimivirus. Virus Res 2006; 117: 145-155.
51. Filee J, Siguier P, Chandler M: I am what I eat and I eat what I am: acquisition of bacterial genes by giant viruses. Trends Genet 2007; 23: 10-15.
52. Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA: The COG database: an updated version includes eukaryotes. BMC Bioinformatics 2003; 4: 41.
53. Dyková I, Fiala I, Lom J, Lukeš J: Perkinsiella amoebae -like endosymbionts of Neoparamoeba spp., relatives of the kinetoplastid Ichthyobodo . Eur J Protistol 2003; 39: 37-52.
54. Frost LS, Leplae R, Summers AO, Toussaint A: Mobile genetic elements: The agents of open source evolution. Nat Rev Microbiol 2005; 3: 722-732.
55. Ton-Hoang B, Guynet C, Ronning DR, Cointin- Marty B, Dyda F, Chandler M: Transposition of ISHp608, member of an unusual family of bacterial insertion sequences. EMBO J 2005; 24: 3325-3338.
56. Guhan N, Muniyappa K: Structural and functional characteristics of homing endonucleases. Crit Rev Biochem Mol Biol 2003; 38: 199-248.
57. Ogata H, Raoult D, Claverie JM: A new example of viral intein in Mimivirus. Virol J 2005; 2: 8.
58. Hirata R, Ohsumk Y, Nakano A, Kawasaki H, Suzuki K, Anraku Y: Molecular structure of a gene, VMA1, encoding the catalytic subunit of H(+)-translocating adenosine triphosphatase from vacuolar membranes of Saccharomyces cerevisiae . J Biol Chem 1990; 265: 6726-6733.
59. Kane PM, Yamashiro CT, Wolczyk DF, Neff N, Goebl M, Stevens TH: Protein splicing converts the yeast TFP1 gene product to the 69-kD subunit of the vacuolar H(+)-adenosine triphosphatase. Science 1990; 250: 651-657.
60. Pietrokovski S: Identification of a virus intein and a possible variation in the proteinsplicing reaction. Curr Biol 1998; 8:R634-R635.
61. Weynberg KD, Allen MJ, Ashelford K, Scanlan DJ, Wilson WH: From small hosts come big viruses: The complete genome of a second Ostreococcus tauri virus, OtV-1. Environ Microbiol 2009; 11: 2821-2839.
62. Williamson SJ, Rusch DB, Yooseph S, Halpern AL, Heidelberg KB, Glass JI, Andrews-Pfannkoch C, Fadrosh D, Miller CS, Sutton G, Frazier M, Venter JC: The Sorcerer II Global Ocean Sampling Expedition: metagenomic characterization of viruses within aquatic microbial samples. PLoS One 2008; 3:e1456.
63. Iyer LM, Makarova KS, Koonin EV, Aravind L: Comparative genomics of the FtsK-HerA superfamily of pumping ATPases: implications for the origins of chromosome segregation, cell division and viral capsid packaging. Nucleic Acids Res 2004; 32: 5260-5279.
64. De Silva FS, Moss B: Origin-independent plasmid replication occurs in vaccinia virus cytoplasmic factories and requires all five known poxvirus replication factors. Virol J 2005; 2: 23.
65. Rojo G, Garcia-Beato R, Vinuela E, Salas ML, Salas J: Replication of African swine fever virus DNA in infected cells. Virology 1999; 257: 524-536.
66. Gubbels MJ, Vaishnava S, Boot N, Dubremetz JF, Striepen B: A MORN-repeat protein is a dynamic component of the Toxoplasma gondii cell division apparatus. J Cell Sci 2006; 119: 2236-2245.
67. Cheng CH, Liu SM, Chow TY, Hsiao YY, Wang DP, Huang JJ, Chen HH: Analysis of the complete genome sequence of the Hz-1 virus suggests that it is related to members of the Baculoviridae. J Virol 2002; 76: 9024-9034.
68. Ibrahim AMA, Choi JY, Je YH, Kim Y: Structure and expression profile of two putative Cotesia plutellae bracovirus genes (CpBV-H4 and CpBV-E94{alpha}) in parasitized Plutella xylostella . J Asia Pacific Entomol 2005; 8: 359-366.
69. Horn M, Wagner M: Bacterial endosymbionts of free-living amoebae. J Eukaryot Microbiol 2004; 51: 509-514.
70. Suzan-Monti M, La Scola B, Barrassi L, Espinosa L, Raoult D: Ultrastructural characterization of the giant volcano-like virus factory of Acanthamoeba polyphaga Mimivirus. PLoS One 2007; 2:e328.
71. Ogata H, La Scola B, Audic S, Renesto P, Blanc G, Robert C, Fournier PE, Claverie JM, Raoult D: Genome sequence of Rickettsia bellii illuminates the role of amoebae in gene exchanges between intracellular pathogens. PLoS Genet 2006; 2:e76.
72. Yao XD, Evans DH: Effects of DNA structure and homology length on vaccinia virus recombination. J Virol 2001; 75: 6923-6932.
73. Willer DO, Yao XD, Mann MJ, Evans DH: In vitro concatemer formation catalyzed by vaccinia virus DNA polymerase. Virology 2000; 278: 562-569.
74. Ball LA: High-frequency homologous recombination in vaccinia virus DNA. J Virol 1987; 61: 1788-1795.
75. Evans DH, Stuart D, McFadden G: High levels of genetic recombination among cotransfected plasmid DNAs in poxvirus-infected mammalian cells. J Virol 1988; 62: 367-375.
76. Tessman I: Genetic recombination of the DNA plant virus PBCV1 in a Chlorella -like alga. Virology 1985; 145: 319-322.
77. Reuven NB, Willcox S, Griffith JD, Weller SK: Catalysis of strand exchange by the HSV-1 UL12 and ICP8 proteins: potent ICP8 recombinase activity is revealed upon resection of dsDNA substrate by nuclease. J Mol Biol 2004; 342: 57-71.
78. Cheng C, Shuman S: Recombinogenic flap ligation pathway for intrinsic repair of topoisomerase IB-induced double-strand breaks. Mol Cell Biol 2000; 20: 8059-8068.
79. Benarroch D, Claverie JM, Raoult D, Shuman S: Characterization of mimivirus DNA topoisomerase IB suggests horizontal gene transfer between eukaryal viruses and bacteria. J Virol 2006; 80: 314-321.
80. Rodriguez-Zaragoza S: Ecology of free-living amoebae. Crit Rev Microbiol 1994; 20: 225-241.
81. Mattana A, Serra C, Mariotti E, Delogu G, Fiori PL, Cappuccinelli P: Acanthamoeba castellanii promotion of in vitro survival and transmission of coxsackie b3 viruses. Eukaryot Cell 2006; 5: 665-671.
82. Audic S, Robert C, Campagna B, Parinello H, Claverie JM, Raoult D, Drancourt M: Genome analysis of Minibacterium massiliensis highlights the convergent evolution of water-living bacteria. PLoS Genet 2007; 3:e138.
83. Moliner C, Raoult D, Fournier PE: Evidence that the intra-amoebal Legionella drancourtii acquired a sterol reductase gene from eukaryotes. BMC Res Notes 2009; 2: 51.
84. Boussau B, Karlberg EO, Frank AC, Legault BA, Andersson SG: Computational inference of scenarios for alpha-proteobacterial genome evolution. Proc Natl Acad Sci USA 2004; 101: 9722-9727.
85. Sakharkar KR, Dhar PK, Chow VT: Genome reduction in prokaryotic obligatory intracellular parasites of humans: a comparative analysis. Int J Syst Evol Microbiol 2004; 54: 1937-1941.
86. Chien M, Morozova I, Shi S, Sheng H, Chen J, Gomez SM, Asamani G, Hill K, Nuara J, Feder M, Rineer J, Greenberg JJ, Steshenko V, Park SH, Zhao B, Teplitskaya E, Edwards JR, Pampou S, Georghiou A, Chou IC, Iannuccilli W, Ulz ME, Kim DH, Geringer-Sameth A, Goldsberry C, Morozov P, Fischer SG, Segal G, Qu X, Rzhetsky A, Zhang P, Cayanis E, De Jong PJ, Ju J, Kalachikov S, Shuman HA, Russo JJ: The genomic sequence of the accidental pathogen Legionella pneumophila . Science 2004; 305: 1966-1968.
87. Cazalet C, Rusniok C, Bruggemann H, Zidane N, Magnier A, Ma L, Tichit M, Jarraud S, Bouchier C, Vandenesch F, Kunst F, Etienne J, Glaser P, Buchrieser C: Evidence in the Legionella pneumophila genome for exploitation of host cell functions and high genome plasticity. Nat Genet 2004; 36: 1165-1173.
88. Horn M, Collingro A, Schmitz-Esser S, Beier CL, Purkhold U, Fartmann B, Brandt P, Nyakatura GJ, Droege M, Frishman D, Rattei T, Mewes HW, Wagner M: Illuminating the evolutionary history of chlamydiae. Science 2004; 304: 728-730.
89. Greub G, Kebbi-Beghdadi C, Bertelli C, Collyn F, Riederer BM, Yersin C, Croxatto A, Raoult D: High throughput sequencing and proteomics to identify immunogenic proteins of a new pathogen: The dirty genome approach. PLoS One 2009; 4:e8423.
90. Schmitz-Esser S, Linka N, Collingro A, Beier CL, Neuhaus HE, Wagner M, Horn M: ATP/ ADP translocases: a common feature of obligate intracellular amoebal symbionts related to Chlamydiae and Rickettsiae. J Bacteriol 2004; 186: 683-691.
91. Tamas I, Klasson L, Canback B, Naslund AK, Eriksson AS, Wernegreen JJ, Sandstrom JP, Moran NA, Andersson SG: 50 million years of genomic stasis in endosymbiotic bacteria. Science 2002; 296: 2376-2379.
92. Merhej V, Royer-Carenzi M, Pontarotti P, Raoult D: Massive comparative genomic analysis reveals convergent evolution of specialized bacteria. Biol Direct 2009; 4: 13.
93. Bruggemann H, Cazalet C, Buchrieser C: Adaptation of Legionella pneumophila to the host environment: role of protein secretion, effectors and eukaryotic-like proteins. Curr Opin Microbiol 2006; 9: 86-94.
94. Walburger A, Koul A, Ferrari G, Nguyen L, Prescianotto-Baschong C, Huygen K, Klebl B, Thompson C, Bacher G, Pieters J: Protein kinase G from pathogenic mycobacteria promotes survival within macrophages. Science 2004; 304: 1800-1804.
95. Meersseman W, Lagrou K, Sciot R, de JJ, Haberler C, Walochnik J, Peetermans WE, van WE: Rapidly fatal Acanthamoeba encephalitis and treatment of cryoglobulinemia. Emerg Infect Dis 2007; 13: 469-471.
96. Abu KY, Gao LY, Stone BJ, Venkataraman C, Harb OS: Invasion of protozoa by Legionella pneumophila and its role in bacterial ecology and pathogenesis. Appl Environ Microbiol 1998; 64: 3127-3133.
97. Barker J, Brown MR: Trojan horses of the microbial world: protozoa and the survival of bacterial pathogens in the environment. Microbiology 1994; 140: 1253-1259.
98. Ghigo E, Kartenbeck J, Lien P, Pelkmans L, Capo C, Mege JL, Raoult D: Ameobal pathogen Mimivirus infects macrophages through phagocytosis. PLoS Pathog 2008; 4:e1000087.
99. Greub G, Raoult D: Microorganisms resistant to free-living amoebae. Clin Microbiol Rev 2004; 17: 413-433.
100. Steenbergen JN, Shuman HA, Casadevall A: Cryptococcus neoformans interactions with amoebae suggest an explanation for its virulence and intracellular pathogenic strategy in macrophages. Proc Natl Acad Sci USA 2001; 98: 15245-15250.
101. La Scola B, Marrie TJ, Auffray JP, Raoult D: Mimivirus in pneumonia patients. Emerg Infect Dis 2005; 11: 449-452.
102. Berger P, Papazian L, Drancourt M, La Scola B, Auffray JP, Raoult D: Ameba-associated microorganisms and diagnosis of nosocomial pneumonia. Emerg Infect Dis 2006; 12: 248-255.
103. Raoult D, Renesto P, Brouqui P: Laboratory infection of a technician by mimivirus. Ann Intern Med 2006; 144: 702-703.
104. Khan M, La Scola B, Lepidi H, Raoult D: Pneumonia in mice inoculated experimentally with Acanthamoeba polyphaga mimivirus. Microb Pathog 2007; 42: 56-61.
105. Vincent A, La Scola B, Forel JM, Pauly V, Raoult D, Papazian L: Clinical significance of a positive serology for mimivirus in patients presenting a suspicion of ventilatorassociated pneumonia. Crit Care Med 2009; 37: 111-118.
106. Monier A, Larsen JB, Sandaa RA, Bratbak G, Claverie JM, Ogata H: Marine mimivirus relatives are probably large algal viruses. Virol J 2008; 5: 12.
107. Claverie JM, Grzela R, Lartigue A, Bernadac A, Nitsche S, Vacelet J, Ogata H, Abergel C: Mimivirus and Mimiviridae: giant viruses with an increasing number of potential hosts, including corals and sponges. J Invertebr Pathol 2009; 101: 172-180.
108. Van Valen L: A new evolutionary law. Evolutionary Theory 1973; 1: 1-30.
109. Suhre K: Gene and genome duplication in Acanthamoeba polyphaga Mimivirus. J Virol 2005; 79: 14095-14101.
110. Zhang J: Evolution by gene duplication: an update. Trends Ecol Evol 2003; 18: 292-298.
111. Hurles M: Gene duplication: The genomic trade in spare parts. PLoS Biol 2004; 2:E206.
112. Fischer D, Eisenberg D: Finding families for genomic ORFans. Bioinformatics 1999; 15: 759-762.
113. Koonin EV, Wolf YI, Nagasaki K, Dolja VV: The complexity of the virus world. Nat Rev Microbiol 2009, E-pub ahead of print.