Viral genome size distribution does not correlate with the antiquity of the host lineages

Frontiers in Ecology and Evolution

Volumn 3, Issue DEC, 2015, Pages

  Campillo Balderas, José A ^a   Lazcano, Antonio ^a,b   Becerra, Arturo ^a  

^a UNIVERSIDAD NACIONAL AUTÓNOMA DE MÉXICO   (Mexico)

^b EL COLEGIO NACIONAL   (Mexico)

Author keywords

Origin of viruses; Viral genome sizes; Viruses and the RNA protein world

Indexed keywords

EID: 84995488627     PISSN: None     EISSN: 2296701X     Source Type: Journal    
DOI: 10.3389/fevo.2015.00143     Document Type: Article

References (47)

1. Agol, V. I. (2010). Which came first, the virus or the cell? Paleontol. J. 44, 728-736. doi: 10.1134/S0031030110070038
2. Baltimore, D. (1971). Expression of animal virus genomes. Bacteriol. Rev. 35, 235-241
3. Berkhout, B., and Haasnoot, J. (2006). The interplay between virus infection and the cellular RNA interference machinery. FEBS Lett. 580, 2896-2902. doi: 10.1016/j.febslet.2006.02.070
4. Beutner, R. (1938). Life's Beginning on the Earth. Baltimore: The Williams & Wilkins Company
5. Boyer, M., Yutin, N., Pagnier, I., Barrassi, L., Fournous, G., Espinosa, L., et al. (2009). Giant Marseillevirus highlights the role of amoebae as a melting pot in emergence of chimeric microorganisms. Proc. Natl. Acad. Sci. U.S.A. 106, 21848-21853. doi: 10.1073/pnas.0911354106
6. Caprari, S., Metzler, S., Lengauer, T., and Kalinina, O. V. (2015). Sequence and structure analysis of distantly-related viruses reveals extensive gene transfer between viruses and hosts and among viruses. Viruses 10, 5388-5409. doi: 10.3390/v7102882
7. Cerutti, H., and Casas-Mollano, J. A. (2006). On the origin and functions of RNA-mediated silencing: from protists to man. Curr. Genet. 50, 81-99. doi: 10.1007/s00294-006-0078-x
8. Colson, P., and Raoult, D. (2010). Gene repertoire of amoeba-associated giant viruses. Intervirology 53, 330-343. doi: 10.1159/000312918
9. Crandall, K. A., Pérez-Losada, M., Christensen, R. G., McClellan, D. A., and Viscidi, R. P. (2006). Phylogenomics and molecular evolution of polyomaviruses. Adv. Exp. Med. Bio. 577, 46-59. doi: 10.1007/0-387-32957-9_3
10. Daros, J.-A., Elena, S. F., and Flores, R. (2006). Viroids: an Ariadne's thread into the RNA labyrinth. EMBO Rep. 7, 593-598. doi: 10.1038/sj.embor.7400706
11. de Villiers, E. M., Fauquet, C., Broker, T. R., Bernard, H. U., and Zur Hausen, H. (2004). Classification of papillomaviruses. Virology 324, 17-27. doi: 10.1016/j.virol.2004.03.033
12. d'Herelle, F. (1926). The Bacteriophage and its Behavior. Baltimore, MD: The Williams & Wilkins Company
13. Duffy, S., and Holmes, E. C. (2008). Phylogenetic evidence for rapid rates of molecular evolution in the single-stranded DNA begomovirus tomato yellow leaf curl virus. J. Virol. 82, 957-965. doi: 10.1128/JVI.01929-07
14. Filee, J. (2013). Route of NCLDV evolution: the genomic accordion. Curr. Opin. Virol. 3, 595-599. doi: 10.1016/j.coviro.2013.07.003
15. Filee, J. (2014). Multiple occurrences of giant virus core genes acquired by eukaryotic genomes: the visible part of the iceberg? Virology 466, 53-59. doi: 10.1016/j.virol.2014.06.004
16. Filée, J., Siguier, P., and 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. doi: 10.1016/j.tig.2006.11.002
17. Fisher, S. (2010). Are RNA viruses vestiges of an RNA world? J. Gen. Philos. Sci. 41, 121-141. doi: 10.1007/s10838-010-9119-8
18. Flores, R., Gago-Zachert, S., Serra, P., Sanjuán, R., and Elena, S. F. (2014). Viroids: Survivors from the RNA World? Annu. Rev. Microbiol. 68, 395-414. doi: 10.1146/annurev-micro-091313-103416
19. Forterre, P. (2006). The origin of viruses and their possible roles in major evolutionary transitions. Virus Res. 117, 5-16. doi: 10.1016/j.virusres.2006.01.010
20. Froissart, R., Wilke, C. O., Montville, R., Remold, S. K., Chao, L., and Turner, P. E. (2004). Co-infection weakens selection against epistatic mutations in RNA viruses. Genetics 168, 9-19. doi: 10.1534/genetics.104.030205
21. Gray, S. M., and Banerjee, N. (1999). Mechanisms of arthropod transmission of plant and animal viruses. Microbiol. Mol. Biol. Rev. 63, 128-148
22. Hendrix, R. W. (2002). Bacteriophages: evolution of the majority. Theor. Popul. Biol. 61, 471-480. doi: 10.1006/tpbi.2002.1590
23. Holmes, E. (2009). The Evolution and Emergence of RNA Viruses. New York, NY: Oxford University Press Inc
24. Iyer, L. A., Balaji, S., Koonin, E. V., and Aravind, L. (2006). Evolutionary genomics of nucleo-cytoplasmic large DNA viruses. Virus Res. 117, 156-184. doi: 10.1016/j.virusres.2006.01.009
25. Jácome, R., Becerra, A., Ponce De León, S., and Lazcano, A. (2015). Structural analysis of monomeric RNA-dependent polymerases: evolutionary and therapeutic implications. PLoS ONE 10:e0139001. doi: 10.1371/journal.pone.0139001
26. Jalasvuori, M., Mattila, S., and Hoikkala, V. (2015). Chasing the origin of viruses: capsid-forming genes as a life-saving preadaptation within a community of early replicators. PLoS ONE 10:e0126094. doi: 10.1371/journal.pone.0126094
27. King, A. M. Q., Lefkowitz, E., Adams, M. J., and Carstens, E. B. (2011). Virus Taxonomy: Classification and Nomenclature of Viruses: Ninth Report of the International Committee on Taxonomy of Viruses. San Diego, CA: Elsevier Academic Press
28. Koonin, E. V., and Dolja, V. V. (2013). A virocentric perspective on the evolution of life. Curr. Opin. Virol. 3, 546-557. doi: 10.1016/j.coviro.2013.06.008
29. Koonin, E. V., Senkevich, T. G., and Dolja, V. V. (2006). The ancient virus world and evolution of cells. Biol. Direct 1, 1-27. doi: 10.1186/1745-6150-1-1
30. Krupovic, M., Prangishvili, D., Hendrix, R. W., and Bamford, D. H. (2011). Genomics of bacterial and archaeal viruses: dynamics within the prokaryotic virosphere. Microbiol. Mol. Biol. Rev. 75, 610-635. doi: 10.1128/MMBR.00011-11
31. Legendre, M., Bartoli, J., Shmakova, L., Jeudy, S., Labadie, K., Adrait, A., et al. (2014). Thirty-thousand-year-old distant relative of giant icosahedral DNA viruses with a pandoravirus morphology. Proc. Natl. Acad. Sci. U.S.A. 111, 4274-4279. doi: 10.1073/pnas.1320670111
32. Letunic, I., and Bork, P. (2007). Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics 23, 127-128. doi: 10.1093/bioinformatics/btl529
33. Lobo, F. P., Mota, B. E. F., Pena, S. D. J., Azevedo, V., Macedo, A. M., Tauch, A., et al. (2009). Virus-host coevolution: common patterns of nucleotide motif usage in Flaviviridae and their hosts. PLoS ONE 4:e6282. doi: 10.1371/journal.pone.0006282
34. Lodish, H. F., Zhou, B., Liu, G., and Chen, C. Z. (2008). Micromanagement of the immune system by microRNAs. Nat. Rev. Immunol. 8, 120-130. doi: 10.1038/nri2252
35. Moreira, D., and Brochier-Armanet, C. (2008). Giant viruses, giant chimeras: the multiple evolutionary histories of Mimivirus genes. BMC Evol. Biol. 8:12. doi: 10.1186/1471-2148-8-12
36. Nasir, A., Kim, K. M., and Caetano-Anolles, G. (2012). Giant viruses coexisted with the cellular ancestors and represent a distinct supergroup along with superkingdoms Archaea, Bacteria and Eukarya. BMC Evol. Biol. 12:156. doi: 10.1186/1471-2148-12-156
37. Nasir, A., Sun, F.-J., Kim, K. M., and Caetano-Anollés, G. (2015). Untangling the origin of viruses and their impact on cellular evolution. Ann. N.Y. Acad. Sci. 1341, 61-74. doi: 10.1111/nyas.12735
38. Obbard, D. J., and Dudas, G. (2014). The genetics of host-virus coevolution in invertebrates. Curr. Opin. Virol. 8, 73-78. doi: 10.1016/j.coviro.2014.07.002
39. Obbard, D. J., Gordon, K. H. J., Buck, A. H., and Jiggins, F. M. (2009). The evolution of RNAi as a defence against viruses and transposable elements. Philos. Trans. R. Soc. B Biol. Sci. 364, 99-115. doi: 10.1098/rstb.2008.0168
40. Parameswaran, P., Sklan, E., Wilkins, C., Burgon, T., Samuel, M. A., Lu, R., et al. (2010). Six RNA viruses and forty-one hosts: viral small RNAs and modulation of small RNA repertoires in vertebrate and invertebrate systems. PLoS Pathog. 6:e1000764. doi: 10.1371/journal.ppat.1000764
41. Pennisi, E. (2013). Ever-bigger viruses shake tree of life. Science 341, 226-227. doi: 10.1126/science.341.6143.226
42. Philippe, N., Legendre, M., Doutre, G., Couté, Y., Poirot, O., Lescot, M., et al. (2013). Pandoraviruses: amoeba viruses with genomes up to 2.5 Mb reaching that of parasitic eukaryotes. Science 341, 281-286. doi: 10.1126/science.1239181
43. Podolsky, S. (1996). The role of the virus in origin-of-life theorizing. J. Hist. Biol. 29, 79-126
44. Raoult, D., Audic, S., Robert, C., Abergel, C., Renesto, P., Ogata, H., et al. (2004). The 1.2-megabase genome sequence of mimivirus. Science 306, 1344-1350. doi: 10.1126/science.1101485
45. Reanney, D. C. (1982). The evolution of RNA viruses. Annu. Rev. Microbiol. 36, 47-73. doi: 10.1146/annurev.mi.36.100182.000403
46. Yutin, N., and Koonin, E. V. (2012). Hidden evolutionary complexity of nucleocytoplasmic large DNA viruses of eukaryotes. Virol. J. 9:161. doi: 10.1186/1743-422X-9-161
47. Yutin, N., Wolf, Y. I., and Koonin, E. V. (2014). Origin of giant viruses from smaller DNA viruses not from a fourth domain of cellular life. Virology 466, 38-52. doi: 10.1016/j.virol.2014.06.032