Eukaryotic large nucleo-cytoplasmic DNA viruses: Clusters of orthologous genes and reconstruction of viral genome evolution

Virology Journal

Volumn 6, Issue , 2009, Pages

  Yutin, Natalya ^a   Wolf, Yuri I ^a   Raoult, Didier ^b   Koonin, Eugene V ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

^b CNRS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; DNA VIRUS; EUKARYOTIC CELL; GENE CLUSTER; GENE SEQUENCE; GENETIC VARIABILITY; GENOME ANALYSIS; HOST CELL; MAXIMUM LIKELIHOOD METHOD; MOLECULAR EVOLUTION; MORPHOGENESIS; NONHUMAN; NUCLEO CYTOPLASMIC LARGE DNA VIRUS; ORTHOLOGY; PHYLOGENY; VIRUS GENE; VIRUS GENOME; VIRUS IDENTIFICATION; VIRUS REPLICATION; AFRICAN SWINE FEVER VIRUS; CELL NUCLEUS; CLASSIFICATION; CYTOPLASM; EUKARYOTE; GENETICS; GENOMICS; IRIDOVIRUS; PHYCODNAVIRIDAE; POXVIRUS; VIROLOGY;

DNA VIRUSES; EUKARYOTA;

PROTEOME; VIRUS PROTEIN;

ASFARVIRIDAE; CELL NUCLEUS; CYTOPLASM; DNA VIRUSES; EUKARYOTA; EVOLUTION, MOLECULAR; GENOME, VIRAL; GENOMICS; IRIDOVIRIDAE; PHYCODNAVIRIDAE; PHYLOGENY; POXVIRIDAE; PROTEOME; VIRAL PROTEINS;

EID: 74549198854     PISSN: None     EISSN: 1743422X     Source Type: Journal    
DOI: 10.1186/1743-422X-6-223     Document Type: Article

References (53)

1. Fields Virology. BN Fields PM Howley DE Griffin RA Lamb MA Martin B Roizman SE Straus DM Knipe (eds.), New York: Lippincott Williams & Wilkins 2001
2. The origin of viruses and their possible roles in major evolutionary transitions. P Forterre, Virus Res 2006 117 1 5 16 10.1016/j.virusres.2006.01. 010 16476498
3. Redefining viruses: lessons from Mimivirus. D Raoult P Forterre, Nat Rev Microbiol 2008 6 4 315 319 10.1038/nrmicro1858 18311164
4. The ancient Virus World and evolution of cells. EV Koonin TG Senkevich VV Dolja, Biol Direct 2006 1 29 10.1186/1745-6150-1-29 16984643
5. Common origin of four diverse families of large eukaryotic DNA viruses. LM Iyer L Aravind EV Koonin, J Virol 2001 75 23 11720 11734 10.1128/JVI.75.23. 11720-11734.2001 11689653
6. Evolutionary genomics of nucleo-cytoplasmic large DNA viruses. LM Iyer S Balaji EV Koonin L Aravind, Virus Res 2006 117 1 156 184 10.1016/j.virusres. 2006.01.009 16494962
7. Unusual life style of giant chlorella viruses. JL Van Etten, Annu Rev Genet 2003 37 153 195 10.1146/annurev.genet.37.110801.143915 14616059
8. Lateral gene transfer, lineage-specific gene expansion and the evolution of Nucleo Cytoplasmic Large DNA viruses. J Filee, J Invertebr Pathol 2009 101 3 169 171 10.1016/j.jip.2009.03.010 19457437
9. The virophage as a unique parasite of the giant mimivirus. B La Scola C Desnues I Pagnier C Robert L Barrassi G Fournous M Merchat M Suzan-Monti P Forterre E Koonin D Raoult, Nature 2008 455 7209 100 104 10.1038/nature07218 18690211
10. The 1.2-megabase genome sequence of Mimivirus. D Raoult S Audic C Robert C Abergel P Renesto H Ogata B La Scola M Suzan JM Claverie, Science 2004 306 5700 1344 1350 10.1126/science.1101485 15486256
11. Mimivirus and its Virophage. JM Claverie C Abergel, Annu Rev Genet 2009 43 49 66 19653859 10.1146/annurev-genet-102108-134255
12. Mimivirus. JM Claverie C Abergel H Ogata, Curr Top Microbiol Immunol 2009 328 89 121 full-text 19216436
13. Genomic and evolutionary aspects of Mimivirus. M Suzan-Monti B La Scola D Raoult, Virus Res 2006 117 1 145 155 10.1016/j.virusres.2005.07.011 16181700
14. Mimivirus and the emerging concept of "giant" virus. JM Claverie H Ogata S Audic C Abergel K Suhre PE Fournier, Virus Res 2006 117 1 133 144 10.1016/j.virusres.2006.01.008 16469402
15. Virology: Gulliver among the Lilliputians. EV Koonin, Curr Biol 2005 15 5 167 169 10.1016/j.cub.2005.02.042 15753027
16. Phylogenetic evidence for extensive lateral acquisition of cellular genes by Nucleocytoplasmic large DNA viruses. J Filee N Pouget M Chandler, BMC Evol Biol 2008 8 320 10.1186/1471-2148-8-320 19036122
17. Giant viruses, giant chimeras: the multiple evolutionary histories of Mimivirus genes. D Moreira C Brochier-Armanet, BMC Evol Biol 2008 8 12 10.1186/1471-2148-8-12 18205905
18. I am what I eat and I eat what I am: acquisition of bacterial genes by giant viruses. J Filee P Siguier M Chandler, Trends Genet 2007 23 1 10 15 10.1016/j.tig.2006.11.002 17109990
19. Giant Marseillevirus highlights the role of amoebae as a melting pot in emergence of chimaeric microorganisms. M Boyer N Yutin I Pagnier L Barrassi G Fournous M Espinosa C Robert A Azza S Sun MG Rossmann M Suzan-Monti B La Scola EV Koonin D Raoult, Proc Natl Acad Sci USA 2009
20. Mimivirus relatives in the Sargasso sea. E Ghedin JM Claverie, Virol J 2005 2 62 10.1186/1743-422X-2-62 16105173
21. Taxonomic distribution of large DNA viruses in the sea. A Monier JM Claverie H Ogata, Genome Biol 2008 9 7 106 10.1186/gb-2008-9-7-r106 18598358
22. Marine mimivirus relatives are probably large algal viruses. A Monier JB Larsen RA Sandaa G Bratbak JM Claverie H Ogata, Virol J 2008 5 12 10.1186/1743-422X-5-12 18215256
23. New dimensions of the virus world discovered through metagenomics. DM Kristensen AR Mushegian VV Dolja EV Koonin, Trends Microbiol 2010
24. Mimivirus and Mimiviridae: giant viruses with an increasing number of potential hosts, including corals and sponges. JM Claverie R Grzela A Lartigue A Bernadac S Nitsche J Vacelet H Ogata C Abergel, J Invertebr Pathol 2009 101 3 172 180 10.1016/j.jip.2009.03.011 19457438
25. Distinguishing homologous from analogous proteins. WM Fitch, Systematic Zoology 1970 19 99 106 10.2307/2412448 5449325
26. Orthologs, Paralogs and Evolutionary Genomics. EV Koonin, Annu Rev Genet 2005 39 309 338 16285863 10.1146/annurev.genet.39.073003.114725 (Pubitemid 43011118)
27. The COG database: an updated version includes eukaryotes. RL Tatusov ND Fedorova JD Jackson AR Jacobs B Kiryutin EV Koonin DM Krylov R Mazumder SL Mekhedov AN Nikolskaya, et al. BMC Bioinformatics 2003 4 41 10.1186/1471-2105-4- 41 12969510
28. A genomic perspective on protein families. RL Tatusov EV Koonin DJ Lipman, Science 1997 278 5338 631 637 10.1126/science.278.5338.631 9381173
29. The cyanobacterial genome core and the origin of photosynthesis. AY Mulkidjanian EV Koonin KS Makarova SL Mekhedov A Sorokin YI Wolf A Dufresne F Partensky H Burd D Kaznadzey R Haselkorn MY Galperin, Proc Natl Acad Sci USA 2006 103 35 13126 13131 10.1073/pnas.0605709103 16924101
30. Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea. KS Makarova AV Sorokin PS Novichkov YI Wolf EV Koonin, Biol Direct 2007 2 33 10.1186/1745-6150-2-33 18042280
31. Comparative genomics, minimal gene-sets and the last universal common ancestor. EV Koonin, Nat Rev Microbiol 2003 1 2 127 136 10.1038/nrmicro751 15035042
32. Computing prokaryotic gene ubiquity: rescuing the core from extinction. RL Charlebois WF Doolittle, Genome Res 2004 14 12 2469 2477 10.1101/gr.3024704 15574825
33. Non-orthologous gene displacement. EV Koonin AR Mushegian P Bork, Trends Genet 1996 12 9 334 336 10.1016/0168-9525(96)20010-1 8855656
34. An approximately unbiased test of phylogenetic tree selection. H Shimodaira, Syst Biol 2002 51 3 492 508 10.1080/10635150290069913 12079646 (Pubitemid 35180700)
35. Remarkable sequence similarity between the dinoflagellate-infecting marine girus and the terrestrial pathogen African swine fever virus. H Ogata K Toyoda Y Tomaru N Nakayama Y Shirai JM Claverie K Nagasaki, Virol J 2009 6 178 10.1186/1743-422X-6-178 19860921
36. Genome trees and the tree of life. YI Wolf IB Rogozin NV Grishin EV Koonin, Trends Genet 2002 18 9 472 479 10.1016/S0168-9525(02)02744-0 12175808
37. Streamlining and large ancestral genomes in Archaea inferred with a phylogenetic birth-and-death model. M Csuros I Miklos, Mol Biol Evol 2009 26 9 2087 2095 10.1093/molbev/msp123 19570746
38. The genome of molluscum contagiosum virus: analysis and comparison with other poxviruses. TG Senkevich EV Koonin JJ Bugert G Darai B Moss, Virology 1997 233 1 19 42 10.1006/viro.1997.8607 9201214
39. Evolution of DNA ligases of Nucleo-Cytoplasmic Large DNA viruses of eukaryotes: a case of hidden complexity. N Yutin EV Koonin, Biology Direct 2009 4 1 51 10.1186/1745-6150-4-51 20021668
40. The manifold phospholipases A of Legionella pneumophila - identification, export, regulation, and their link to bacterial virulence. S Banerji P Aurass A Flieger, Int J Med Microbiol 2008 298 3-4 169 181 10.1016/j.ijmm.2007.11.004 18178130
41. A duplicated catalytic motif in a new superfamily of phosphohydrolases and phospholipid synthases that includes poxvirus envelope proteins. EV Koonin, Trends Biochem Sci 1996 21 7 242 243 8755242
42. Similarities in the induction of post-Golgi vesicles by the vaccinia virus F13L protein and phospholipase D. M Husain B Moss, J Virol 2002 76 15 7777 7789 10.1128/JVI.76.15.7777-7789.2002 12097590
43. The Big Bang of picorna-like virus evolution antedates the radiation of eukaryotic supergroups. EV Koonin YI Wolf K Nagasaki VV Dolja, Nat Rev Microbiol 2008 6 12 925 939 10.1038/nrmicro2030 18997823
44. GeneMark.hmm: new solutions for gene finding. AV Lukashin M Borodovsky, Nucleic Acids Res 1998 26 4 1107 1115 10.1093/nar/26.4.1107 9461475
45. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. SF Altschul TL Madden AA Schaffer J Zhang Z Zhang W Miller DJ Lipman, Nucleic Acids Res 1997 25 17 3389 3402 10.1093/nar/25.17.3389 9254694
46. MUSCLE: multiple sequence alignment with high accuracy and high throughput. RC Edgar, Nucleic Acids Res 2004 32 5 1792 1797 10.1093/nar/gkh340 15034147
47. CD-Search: protein domain annotations on the fly. A Marchler-Bauer SH Bryant, Nucleic Acids Res 2004 32 Web Server 327 331 10.1093/nar/gkh454 15215404
48. TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics. G Jobb A von Haeseler K Strimmer, BMC Evol Biol 2004 4 18 10.1186/1471-2148-4-18 15222900
49. A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. S Whelan N Goldman, Mol Biol Evol 2001 18 5 691 699 11319253
50. TOPD/FMTS: a new software to compare phylogenetic trees. P Puigbo S Garcia-Vallve JO McInerney, Bioinformatics 2007 23 12 1556 1558 10.1093/bioinformatics/btm135 17459965
51. Search for a 'Tree of Life' in the thicket of the phylogenetic forest. P Puigbo YI Wolf EV Koonin, J Biol 2009 8 6 59 10.1186/jbiol159 19594957
52. Inferring phylogenies from protein sequences by parsimony, distance, and likelihood methods. J Felsenstein, Methods Enzymol 1996 266 418 427 full-text 8743697
53. A probabilistic model for gene content evolution with duplication, loss, and horizontal transfer. M Csuros I Miklos, Lecture Notes in Computer Science 2006 3909 206 220 full-text