Low frequency of paleoviral infiltration across the avian phylogeny

Genome Biology

Volumn 15, Issue 12, 2014, Pages

  Cui, Jie ^a,h   Zhao, Wei ^b   Huang, Zhiyong ^b   Jarvis, Erich D ^c   Thomas, M ^d,g   Walker, Peter J ^e   Holmes, Edward C ^a   Zhang, Guojie ^b,f  

^a University of Sydney   (Australia)

^b BGI SHENZHEN   (China)

^c DUKE UNIVERSITY MEDICAL CENTER   (United States)

^d UNIVERSITY OF COPENHAGEN   (Denmark)

^e CSIRO   (Australia)

^f UNIVERSITY OF COPENHAGEN   (Denmark)

^g CURTIN UNIVERSITY   (Australia)

^h DUKE NUS MEDICAL SCHOOL   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL; BIRD; CLASSIFICATION; DNA SEQUENCE; GENETICS; GENOME; GENOME SIZE; MOLECULAR EVOLUTION; PHYLOGENY; VIROLOGY; VIRUS;

ANIMALS; BIRDS; EVOLUTION, MOLECULAR; GENOME; GENOME SIZE; PHYLOGENY; SEQUENCE ANALYSIS, DNA; VIRUSES;

EID: 84996528945     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/s13059-014-0539-3     Document Type: Article

References (52)

1. Weiss RA: The discovery of endogenous retroviruses. Retrovirology 2006, 3:67.
2. Katzourakis A, Gifford RJ: Endogenous viral elements in animal genomes. PLoS Genet 2010, 6:e1001191.
3. Kazazian HH Jr: Mobile elements: drivers of genome evolution. Science 2004, 303:1626-1632.
4. Jern P, Coffin JM: Effects of retroviruses on host genome function. Annu Rev Genet 2008, 42:709-732.
5. Emerman M, Malik HS: Paleovirology-modern consequences of ancient viruses. PLoS Biol 2010, 8:e1000301.
6. Feschotte C, Gilbert C: Endogenous viruses: insights into viral evolution and impact on host biology. Nat Rev Genet 2012, 13:283-296.
7. Stoye JP: Studies of endogenous retroviruses reveal a continuing evolutionary saga. Nat Rev Microbiol 2012, 10:395-406.
8. Herniou E, Martin J, Miller K, Cook J, Wilkinson M, Tristem M: Retroviral diversity and distribution in vertebrates. J Virol 1997, 71:437-443.
9. Gilbert C, Feschotte C: Genomic fossils calibrate the long-term evolution of hepadnaviruses. PLoS Biol 2010, 8:e1000495.
10. Cui J, Holmes EC: Endogenous Hepadnaviruses in the genome of the budgerigar (Melopsittacus undulatus) and the evolution of avian hepadnaviruses. J Virol 2012, 86:7688-7691.
11. Suh A, Brosius J, Schmitz J, Kriegs JO: The genome of a Mesozoic paleovirus reveals the evolution of hepatitis B viruses. Nat Commun 2013, 4:1791.
12. Bolisetty M, Blomberg J, Benachenhou F, Sperber G, Beemon K: Unexpected diversity and expression of avian endogenous retroviruses. mBio 2012, 3:e00344-12.
13. Zhang G, Li C, Li Q, Li B, Larkin DM, Lee C, Storz JF, Antunes A, Greenwold MJ, Meredith RW, Ödeen A, Cui J, Zhou Q, Xu L, Pan H, Wang Z, Jin L, Zhang P, Hu H, Yang W, Hu J, Xiao J, Yang Z, Liu Y, Xie Q, Yu H, Lian J, Wen P, Zhang F, Li H, et al: Comparative genomics reveals insights into avian genome evolution and adaptation. Science 2014, 346:1311-1320.
14. Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SY, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, da Fonseca RR, Li J, Zhang F, Li H, Zhou L, Narula N, Liu L, Ganapathy G, Boussau B, Bayzid MS, Zavidovych V, Subramanian S, Gabaldón T, Capella-Gutiérrez S, Huerta-Cepas J, Rekepalli B, Munch K, Schierup M, et al: Whole-genome analyses resolve early branches in the tree of life of modern birds. Science 2014, 346:1320-1331.
15. Robertson BH, Margolis HS: Primate hepatitis B viruses - genetic diversity, geography and evolution. Rev Med Virol 2002, 12:133-141.
16. Hackett SJ, Kimball RT, Reddy S, Bowie RC, Braun EL, Braun MJ, Chojnowski JL, Cox WA, Han KL, Harshman J, Huddleston CJ, Marks BD, Miglia KJ, Moore WS, Sheldon FH, Steadman DW, Witt CC, Yuri T: A phylogenomic study of birds reveals their evolutionary history. Science 2008, 320:1763-1768.
17. Horie M, Honda T, Suzuki Y, Kobayashi Y, Daito T, Oshida T, Ikuta K, Jern P, Gojobori T, Coffin JM, Tomonaga K: Endogenous non-retroviral RNA virus elements in mammalian genomes. Nature 2010, 463:84-87.
18. Belyi VA, Levine AJ, Skalka AM: Unexpected inheritance: multiple integrations of ancient bornavirus and ebolavirus/marburgvirus sequences in vertebrate genomes. PLoS Pathog 2010, 6:e1001030.
19. de la Torre JC: Molecular biology of borna disease virus: prototype of a new group of animal viruses. J Virol 1994, 68:7669-7675.
20. VandeWoude S, Richt JA, Zink MC, Rott R, Narayan O, Clements JE: A borna virus cDNA encoding a protein recognized by antibodies in humans with behavioral diseases. Science 1990, 250:1278-1281.
21. Holmes EC: The evolution of endogenous viral elements. Cell Host Microbe 2011, 10:368-377.
22. Belyi VA, Levine AJ, Skalka AM: Sequences from ancestral single-stranded DNA viruses in vertebrate genomes: the parvoviridae and circoviridae are more than 40 to 50 million years old. J Virol 2010, 84:12458-12462.
23. Lehmann HW, von Landenberg P, Modrow S: Parvovirus B19 infection and autoimmune disease. Autoimmun Rev 2003, 2:218-223.
24. Finnegan DJ: Retrotransposons. Curr Biol 2012, 22:R432-R437.
25. Organ CL, Shedlock AM, Meade A, Pagel M, Edwards SV: Origin of avian genome size and structure in non-avian dinosaurs. Nature 2007, 446:180-184.
26. Animal Genome Size Database. [http://www.genomesize.com/]
27. Lipkin WI: The changing face of pathogen discovery and surveillance. Nat Rev Microbiol 2013, 11:133-141.
28. Cui J, Tachedjian M, Wang L, Tachedjian G, Wang LF, Zhang S: Discovery of retroviral homologs in bats: implications for the origin of mammalian gammaretroviruses. J Virol 2012, 86:4288-4293.
29. Niewiadomska AM, Gifford RJ: The extraordinary evolutionary history of the reticuloendotheliosis viruses. PLoS Biol 2013, 11:e1001642.
30. Griffin DK, Robertson LB, Tempest HG, Skinner BM: The evolution of the avian genome as revealed by comparative molecular cytogenetics. Cytogenet Genome Res 2007, 117:64-77.
31. International Chicken Genome Sequencing Consortium: Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 2004, 432:695-716.
32. Warren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LW, Künstner A, Searle S, White S, Vilella AJ, Fairley S, Heger A, Kong L, Ponting CP, Jarvis ED, Mello CV, Minx P, Lovell P, Velho TA, Ferris M, Balakrishnan CN, Sinha S, Blatti C, London SE, Li Y, Lin YC, George J, Sweedler J, Southey B, Gunaratne P, Watson M, et al: The genome of a songbird. Nature 2010, 464:757-762.
33. Dalloul RA, Long JA, Zimin AV, Aslam L, Beal K, Le Blomberg A, Bouffard P, Burt DW, Crasta O, Crooijmans RP, Cooper K, Coulombe RA, De S, Delany ME, Dodgson JB, Dong JJ, Evans C, Frederickson KM, Flicek P, Florea L, Folkerts O, Groenen MA, Harkins TT, Herrero J, Hoffmann S, Megens HJ, Jiang A, de Jong P, Kaiser P, Kim H, et al: Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. PLoS Biol 2010, 8:e1000475.
34. Flicek P, Ahmed I, Amode MR, Barrell D, Beal K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fairley S, Fitzgerald S, Gil L, García-Girón C, Gordon L, Hourlier T, Hunt S, Juettemann T, Kähäri AK, Keenan S, Komorowska M, Kulesha E, Longden I, Maurel T, McLaren WM, Muffato M, Nag R, Overduin B, Pignatelli M, Pritchard B, Pritchard E, et al: Ensembl 2013. Nucleic Acids Res 2013, 41:D48-D55.
35. CoGe database. [http://genomevolution.org/CoGe/]
36. Phylogenomics analysis of birds. [http://phybirds.genomics.org.cn/]
37. King AMQ, Adams MJ, Carstens EB, Lefkowitz EJ: Virus Taxonomy: Classification and Nomenclature of Viruses: Ninth Report of the International Committee on Taxonomy of Viruses. San Diego: Elsevier Academic Press; 2012.
38. RefSeq: NCBI reference sequence database. [http://www.ncbi.nlm.nih.gov/refseq/]
39. Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, Forslund K, Holm L, Sonnhammer EL, Eddy SR, Bateman A: The Pfam protein families database. Nucleic Acids Res 2010, 38:D211-D222.
40. Birney E, Clamp M, Durbin R: GeneWise and genomewise. Genome Res 2004, 14:988-995.
41. Smit AFA, Hubley R, Green P: RepeatMasker Open-3.0. [http://www.repeatmasker.org]
42. Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW: GenBank. Nucleic Acids Res 2013, 41:D36-D42.
43. Edgar RC: MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004, 32:1792-1797.
44. Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O: New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 2010, 59:307-321.
45. Darriba D, Taboada GL, Doallo R, Posada D: ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics 2011, 27:1164-1165.
46. The R Project for Statistical Computing. [http://www.r-project.org]
47. Maddison WP, Maddison DR: Mesquite: a modular system for evolutionary analysis. Version 2.75. [http://mesquiteproject.org]
48. Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst J, Jordan G, Mauceli E, Ward LD, Lowe CB, Holloway AK, Clamp M, Gnerre S, Alföldi J, Beal K, Chang J, Clawson H, Cuff J, Di Palma F, Fitzgerald S, Flicek P, Guttman M, Hubisz MJ, Jaffe DB, Jungreis I, Kent WJ, Kostka D, Lara M, et al: A high-resolution map of human evolutionary constraint using 29 mammals. Nature 2011, 478:476-482.
49. Ho LST, Ané C: A linear-time algorithm for Gaussian and non-Gaussian trait evolution models. Syst Biol 2014, 63:397-408.
50. Legendre P, Desdevises Y, Bazin E: A statistical test for host-parasite coevolution. Syst Biol 2002, 51:217-234.
51. Meier-Kolthoff JP, Auch AF, Huson DH, Göker M: COPYCAT: cophylogenetic analysis tool. Bioinformatics 2007, 23:898-900.
52. The avian phylogenomic project data. [http://gigadb.org/dataset/101000]