Comparative paleovirological analysis of crustaceans identifies multiple widespread viral groups

Mobile DNA

Volumn 6, Issue 1, 2015, Pages

  Metegnier, Gabriel ^a   Becking, Thomas ^a   Chebbi, Mohamed Amine ^a   Giraud, Isabelle ^a   Moumen, Bouziane ^a   Schaack, Sarah ^b   Cordaux, Richard ^a   Gilbert, Clément ^a  

^a UNIVERSITÉ DE POITIERS   (France)

^b REED COLLEGE   (United States)

Author keywords

Bunyaviridae; Circoviridae; Copepoda; Crustacea; Endogenous viral elements; Mononegavirales; Paleovirology; Parvoviridae; Totiviridae; Virus

Indexed keywords

ARMADILLIDIUM NASATUM; ARMADILLIDIUM VULGARE; ARTICLE; BUNYAVIRIDAE; CIRCOVIRIDAE; COMPARATIVE STUDY; CRUSTACEA; DAPHNIA PULEX; DAPHNIA PULICARIA; EURYTEMORA AFFINIS; GENE INSERTION; GENETIC VARIABILITY; GENOME ANALYSIS; HYALELLA AZTECA; LEPEOPHTHEIRUS SALMONIS; MOLECULAR PHYLOGENY; MONONEGAVIRALES; NONHUMAN; NUCLEOTIDE SEQUENCE; ORTHOLOGY; PARVOVIRIDAE; PRIORITY JOURNAL; TOTIVIRIDAE; VIROLOGY; VIRUS IDENTIFICATION;

EID: 84941623143     PISSN: None     EISSN: 17598753     Source Type: Journal    
DOI: 10.1186/s13100-015-0047-3     Document Type: Article

References (70)

1. Willner D, Hugenholtz P. From deep sequencing to viral tagging: Recent advances in viral metagenomics. Bioessays. 2013;35:436-42.
2. Suttle C. Viruses in the sea. Nature. 2005;437:356-61.
3. Breitbart M, Rohwer F. Here a virus, there a virus, everywhere the same virus? Trends Microbiol. 2005;13:278-84.
4. Kristensen DM, Mushegian AR, Dolja VV, Koonin EV. New dimensions of the virus world discovered through metagenomics. Trends Microbiol. 2010;18:11-9.
5. Zilber-Rosenberg I, Rosenberg E. Role of microorganisms in the evolution of animals and plants: the hologenome theory of evolution. FEMS Microbiol Rev. 2008;32:723-35.
6. Roossinck MJ. Move over, bacteria! Viruses make their mark as mutualistic microbial symbionts. J Virol. 2015;89:6532-5.
7. Bamford DH, Grimes JM, Stuart DI. What does structure tell us about virus evolution? Curr Opin Struct Biol. 2005;15:655-63.
8. Forterre P, Prangishvili D. The great billion-year war between ribosome- and capsid-encoding organisms (cells and viruses) as the major source of evolutionary novelties. Ann N Y Acad Sci. 2009;1178:65-77.
9. Koonin E, Senkevich T, Dolja V. The ancient virus world and evolution of cells. Biol Direct. 2006;1:29.
10. Nasir A, Sun FJ, Kim KM, Caetano-Anollés G. Untangling the origin of viruses and their impact on cellular evolution. Ann N Y Acad Sci. 2015;1341:61-74.
11. Katzourakis A, Gifford RJ. Endogenous viral elements in animal genomes. PLoS Genet. 2010;6:e1001191.
12. Feschotte C, Gilbert C. Endogenous viruses: insights into viral evolution and impact on host biology. Nat Rev Genet. 2012;13:283-96.
13. Thézé J, Leclercq S, Moumen B, Cordaux R, Gilbert C. Remarkable diversity of endogenous viruses in a crustacean genome. Genome Biol Evol. 2014;6:2129-40.
14. Ballinger MJ, Bruenn JA, Kotov AA, Taylor DJ. Selectively maintained paleoviruses in Holarctic water fleas reveal an ancient origin for phleboviruses. Virology. 2013;446:276-82.
15. Geering ADW, Maumus F, Copetti D, Choisne N, Zwickl DJ, Zytnicki M, et al. Endogenous florendoviruses are major components of plant genomes and hallmarks of virus evolution. Nat Commun. 2014;5:5269.
16. Zhuo X, Rho M, Feschotte C. Genome-wide characterization of endogenous Retroviruses in the bat Myotis lucifugus reveals recent and diverse infections. J Virol. 2013;87:8493-501.
17. King AMQ, Lefkowitz E, Adams MJ, Carstens EB. Virus Taxonomy: Ninth Report of the International Committee on Taxonomy of Viruses. Boston (MA): Elsevier; 2011.
18. Li C-X, Shi M, Tian J-H, Lin X-D, Kang Y-J, Chen L-J, et al. Unprecedented genomic diversity of RNA viruses in arthropods reveals the ancestry of negative-sense RNA viruses. eLife. 2015;4.
19. Økland AL, Nylund A, Øvergärd A-C, Blindheim S, Watanabe K, Grotmol S, et al. Genomic characterization and phylogenetic position of two new species in Rhabdoviridae infecting the parasitic copepod, salmon louse (Lepeophtheirus salmonis). PLoS One. 2014;9:e112517.
20. Zawar-Reza P, Argüello-Astorga GR, Kraberger S, Julian L, Stainton D, Broady PA, et al. Diverse small circular single-stranded DNA viruses identified in a freshwater pond on the McMurdo Ice Shelf (Antarctica). Infect Genet Evol. 2014;26:132-8.
21. Dayaram A, Goldstien S, Argüello-Astorga GR, Zawar-Reza P, Gomez C, Harding JS, et al. Diverse small circular DNA viruses circulating amongst estuarine molluscs. Infect Genet Evol. 2015;31:284-95.
22. Rosario K, Dayaram A, Marinov M, Ware J, Kraberger S, Stainton D, et al. Diverse circular ssDNA viruses discovered in dragonflies (Odonata: Epiprocta). J Gen Virol. 2012;93(Pt 12):2668-81.
23. Boublik Y, Jousset F-X, Bergoin M. Complete nucleotide sequence and genomic organization of the Aedes albopictus Parvovirus (AaPV) pathogenic for Aedes aegypti larvae. Virology. 1994;200:752-63.
24. Sivaram A, Barde P, Kumar SRP, Yadav P, Gokhale M, Basu A, et al. Isolation and characterization of densonucleosis virus from Aedes aegypti mosquitoes and its distribution in India. Intervirology. 2009;52:1-7.
25. Bonami J-R, Trumper B, Mari J, Brehelin M, Lightner DV. Purification and characterization of the infectious hypodermal and haematopoietic necrosis virus of penaeid shrimps. J Gen Virol. 1990;71:2657-64.
26. Tang KFJ, Lightner DV. Infectious hypodermal and hematopoietic necrosis virus (IHHNV)-related sequences in the genome of the black tiger prawn Penaeus monodon from Africa and Australia. Virus Res. 2006;118:185-91.
27. Isawa H, Kuwata R, Hoshino K, Tsuda Y, Sakai K, Watanabe S, et al. Identification and molecular characterization of a new nonsegmented double-stranded {RNA} virus isolated from Culex mosquitoes in Japan. Virus Res. 2011;155:147-55.
28. Poulos BT, Tang KFJ, Pantoja CR, Bonami JR, Lightner DV. Purification and characterization of infectious myonecrosis virus of penaeid shrimp. J Gen Virol. 2006;87:987-96.
29. Wu Q, Luo Y, Lu R, Lau N, Lai EC, Li W-X, et al. Virus discovery by deep sequencing and assembly of virus-derived small silencing RNAs. Proc Natl Acad Sci. 2010;107:1606-11.
30. Zhai Y, Attoui H, Mohd Jaafar F, Wang H, Cao Y, Fan S, et al. Isolation and full-length sequence analysis of Armigeres subalbatus totivirus, the first totivirus isolate from mosquitoes representing a proposed novel genus (Artivirus) of the family Totiviridae. J Gen Virol. 2010;91:2836-45.
31. Overstreet RM, Jovonovich J, Ma H. Parasitic crustaceans as vectors of viruses, with an emphasis on three penaeid viruses. Integr Comp Biol. 2009;49:127-41.
32. Stentiford GD, Bonami J-R, Alday-Sanz V. A critical review of susceptibility of crustaceans to Taura syndrome, Yellowhead disease and White Spot Disease and implications of inclusion of these diseases in European legislation. Aquaculture. 2009;291:1-17.
33. Lightner DV, Redman RM, Bell TA. Infectious hypodermal and hematopoietic necrosis, a newly recognized virus disease of penaeid shrimp. J Invertebr Pathol. 1983;42:62-70.
34. Williams T. Natural invertebrate hosts of iridoviruses (Iridoviridae). Neotrop Entomol. 2008;37:615-32.
35. Cole A, Morris TJ. A new iridovirus of two species of terrestrial isopods, Armadillidium vulgare and Porcellio scaber. Intervirology. 1980;14:21-30.
36. Federici BA. Isolation of an iridovirus from two terrestrial isopods, the pill bug, Armadillidium vulgare, and the sow bug, Porcellio dilatatus. J Invertebr Pathol. 1980;36:373-81.
37. Lupetti P, Montesanto G, Ciolfi S, Marri L, Gentile M, Paccagnini E, et al. Iridovirus infection in terrestrial isopods from Sicily (Italy). Tissue and Cell. 2013;45:321-7.
38. Dunlap DS, Ng TFF, Rosario K, Barbosa JG, Greco AM, Breitbart M, et al. Molecular and microscopic evidence of viruses in marine copepods. Proc Natl Acad Sci. 2013;110:1375-80.
39. Vandel A. Isopodes terrestres (Deuxième partie). Faune de France. 1962; 66
40. Rozenberg A, Brand P, Rivera N, Leese F, Schubart C. Characterization of fossilized relatives of the White Spot Syndrome Virus in genomes of decapod crustaceans. BMC Evol Biol. 2015;15:142.
41. Shangjin C, Cortey M, Segalés J. Phylogeny and evolution of the NS1 and VP1/VP2 gene sequences from porcine parvovirus. Virus Res. 2009;140(1-2):209-15.
42. Zhang Z, Jia R, Lu Y, Wang M, Zhu D, Chen S, et al. Identification, genotyping, and molecular evolution analysis of duck circovirus. Gene. 2013;529(2):288-95.
43. Huang X, Liu L, Du Y, Wu W, Wang H, Su J, et al. The evolutionary history and spatiotemporal dynamics of the fever, thrombocytopenia and leukocytopenia syndrome virus (FTLSV) in China. PLoS Negl Trop Dis. 2014;8:e3237.
44. Park DJ, Dudas G, Wohl S, Goba A, Whitmer SL, Andersen KG, et al. Ebola virus epidemiology, transmission, and evolution during seven months in Sierra Leone. Cell. 2015;161(7):1516-26.
45. Trinidad L, Blasdell KR, Joubert DA, Davis SS, Melville L, Kirkland PD, et al. Evolution of bovine ephemeral fever virus in the Australian episystem. J Virol. 2014;88:1525-35.
46. Bidokhti MRM, Trävén M, Krishna NK, Munir M, Belák S, Alenius S, et al. Evolutionary dynamics of bovine coronaviruses: natural selection pattern of the spike gene implies adaptive evolution of the strains. J Gen Virol. 2013;94:2036-49.
47. Dupeyron M, Leclercq S, Cerveau N, Bouchon D, Gilbert C. Horizontal transfer of transposons between and within crustaceans and insects. Mobile DNA. 2014;5:4.
48. Knowlton N, Weigt LA. New dates and new rates for divergence across the Isthmus of Panama. Proceedings of the Royal Society of London B: Biological Sciences. 1998;265:2257-63.
49. J. Romiguier J, Gayral P, Ballenghien M, Bernard A, Cahais V, Chenuil A, et al. Comparative population genomics in animals uncovers the determinants of genetic diversity. Nature. 2014;515:261-3.
50. Herniou EA, Huguet E, Thézé J, Bézier A, Periquet G, Drezen J-M. When parasitic wasps hijacked viruses: genomic and functional evolution of polydnaviruses. Philos Trans R Soc Lond B Biol Sci. 2013;368:20130051.
51. Lavialle C, Cornelis G, Dupressoir A, Esnault C, Heidmann O, Vernochet C, et al. Paleovirology of "Syncytins", retroviral env genes exapted for a role in placentation. Philos Trans R Soc Lond B Biol Sci. 2013;368:20120507.
52. Esnault C, Cornelis G, Heidmann O, Heidmann T. Differential evolutionary fate of an ancestral primate endogenous Retrovirus envelope gene, the EnvV Syncytin, captured for a function in placentation. PLoS Genet. 2013;9:e1003400.
53. Lee CE. Rapid and repeated invasions of freshwater by the copepod Eurytemora affinis. Evolution. 1999;53:1423-34.
54. Gustavsen JA, Winget DM, Tian X, Suttle CA. High temporal and spatial diversity in marine RNA viruses implies that they have an important role in mortality and structuring plankton communities. Frontiers in microbiology. 2014;5:703.
55. Jakob E, Barker DE, Garver KA. Vector potential of the salmon louse Lepeophtheirus salmonis in the transmission of infectious haematopoietic necrosis virus (IHNV). Dis Aquat Organ. 2011;97:155-65.
56. Mendoza-Cano F, Sánchez-Paz A, Terán-Díaz B, Galván-Alvarez D, Encinas-García T, Enríquez-Espinoza T, et al. The endemic copepod Calanus pacificus californicus as a potential vector of White Spot Syndrome Virus. J Aquat Anim Health. 2014;26:113-7.
57. Frada MJ, Schatz D, Farstey V, Ossolinski JE, Sabanay H, Ben-Dor S, et al. Zooplankton may serve as transmission vectors for viruses infecting algal blooms in the ocean. Curr Biol. 2014;24:2592-7.
58. Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience. 2012;1:18.
59. Smit AFA, Hubley R. RepeatModeler Open-1.0. 2008-2015. http://www.repeatmasker.org 2015.
60. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25:3389-402.
61. Filée J. Route of NCLDV evolution: the genomic accordion. Current Opinion in Virology. 2013;3:595-9.
62. Filée J, Chandler M. Gene exchange and the origin of giant viruses. Intervirology. 2010;53:354-61.
63. Holzerlandt R, Orengo C, Kellam P, Albà MM. Identification of new herpesvirus gene homologs in the Human genome. Genome Res. 2002;12:1739-48.
64. Hall T. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser. 1999;41:95-8.
65. Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol. 2011;7:539.
66. Whelan S, Goldman N. A general empirical model of protein evolution derived from multiple protein families using a Maximum-Likelihood approach. Mol Biol Evol. 2001;18:691-9.
67. Stamatakis A. RAxML-VI-HPC: Maximum Likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 2006;22:2688-90.
68. Kocher TD, Thomas WK, Meyer A, Edwards SV, Pääbo S, Villablanca FX, et al. Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. Proc Natl Acad Sci. 1989;86:6196-200.
69. Bao W, Kojima KK, Kohany O. Repbase Update, a database of repetitive elements in eukaryotic genomes. Mob DNA. 2015;6:11.
70. Kotov AA, Taylor DJ. Mesozoic fossils (145 Mya) suggest the antiquity of the subgenera of Daphnia andtheir coevolution with chaoborid predators. BMC Evol Biol. 2011;11:129.