Early Mesozoic Coexistence of Amniotes and Hepadnaviridae

PLoS Genetics

Volumn 10, Issue 12, 2014, Pages

  Suh, Alexander ^a   Weber, Claudia C ^a   Kehlmaier, Christian ^b   Braun, Edward L ^c   Green, Richard E ^d   Fritz, Uwe ^b   Ray, David A ^e,f,g   Ellegren, Hans ^a  

^a UPPSALA UNIVERSITY   (Sweden)

^b SENCKENBERG RESEARCH INSTITUTE   (Germany)

^c UNIVERSITY OF FLORIDA   (United States)

^d University of California Santa Cruz   (United States)

^e MISSISSIPPI STATE UNIVERSITY   (United States)

^f MISSISSIPPI STATE UNIVERSITY   (United States)

^g TEXAS TECH UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; AMNIOTE; ARTICLE; CROCODILIAN; FOSSIL ANIMAL; GENE LOCUS; GENE STRUCTURE; GENETIC ASSOCIATION; GENETIC CONSERVATION; HEPADNAVIRIDAE; HEPATITIS B; HOST RANGE; MESOZOIC; NONHUMAN; OPEN READING FRAME; ORTHOHEPADNAVIRUS; PALEOGENE; PHYLOGENY; PROTEIN DOMAIN; PROTEIN MOTIF; REVERSE TRANSCRIPTION; SEQUENCE ALIGNMENT; SNAKE; SPECIES COEXISTENCE; TURTLE; VIRUS ASSEMBLY; VIRUS GENOME; VIRUS REPLICATION; ANIMAL; BIRD; CLASSIFICATION; CONFORMATION; FOSSIL; GENETICS; GENOME; GENOMICS; HEPATITIS B VIRUS; ISOLATION AND PURIFICATION; MAMMAL; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; VIROLOGY;

AMNIOTA; ANIMALIA; AVES; CROCODYLIDAE (ALL CROCODILES); DNA VIRUSES; HEPADNAVIRIDAE; HEPATITIS B VIRUS; MAMMALIA; TESTUDINES; VERTEBRATA;

ALLIGATORS AND CROCODILES; AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; BIRDS; EVOLUTION, MOLECULAR; FOSSILS; GENOME; GENOMICS; HEPADNAVIRIDAE; HEPATITIS B VIRUS; MAMMALS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PHYLOGENY; SNAKES; TURTLES;

EID: 84919663851     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1004559     Document Type: Article

References (80)

1. Weiss RA, Stoye JP, (2013) Our viral inheritance. Science 340: 820–821.
2. Katzourakis A, Gifford RJ, (2010) Endogenous viral elements in animal genomes. PLoS Genetics 6: e1001191.
3. Johnson WE, (2010) Endless forms most viral. PLoS Genetics 6: e1001210.
4. Holmes EC, (2011) The evolution of endogenous viral elements. Cell Host & Microbe 10: 368–377.
5. Feschotte C, Gilbert C, (2012) Endogenous viruses: insights into viral evolution and impact on host biology. Nature Reviews Genetics 13: 283–296.
6. Genome 10K Community of Scientists (2009) Genome 10K: a proposal to obtain whole-genome sequence for 10,000 vertebrate species. Journal of Heredity 100: 659–674.
7. Ellegren H, (2014) Genome sequencing and population genomics in non-model organisms. Trends in Ecology & Evolution 29: 51–63.
8. Patel MR, Emerman M, Malik HS, (2011) Paleovirology – ghosts and gifts of viruses past. Current Opinion in Virology 1: 304–309.
9. Katzourakis A, Gifford RJ, Tristem M, Gilbert MTP, Pybus OG, (2009) Macroevolution of complex retroviruses. Science 325: 1512.
10. Suh A, Brosius J, Schmitz J, Kriegs JO, (2013) The genome of a Mesozoic paleovirus reveals the evolution of hepatitis B viruses. Nature Communications 4: 1791.
11. Belyi VA, Levine AJ, Skalka AM, (2010) Unexpected inheritance: multiple integrations of ancient Bornavirus and Ebolavirus/Marburgvirus sequences in vertebrate genomes. PLoS Pathogens 6: e1001030.
12. Piasecki T, Harkins GW, Chrząstek K, Julian L, Martin DP, et al. (2013) Avihepadnavirus diversity in parrots is comparable to that found amongst all other avian species. Virology 438: 98–105.
13. Drexler JF, Geipel A, König A, Corman VM, van Riel D, et al. (2013) Bats carry pathogenic hepadnaviruses antigenically related to hepatitis B virus and capable of infecting human hepatocytes. Proceedings of the National Academy of Sciences 110: 16151–16156.
14. Mason WS, Gerlich WH, Taylor JM, Kann M, Mizokami T, et al. (2011) Family Hepadnaviridae. In: King AMQ, Adams MJ, Carstens EB, Lefkowitz EJ, editors. Virus Taxonomy: Classification and Nomenclature of Viruses (Ninth Report of the International Committee on Taxonomy of Viruses). Amsterdam: Elsevier. pp. 445–455.
15. Paraskevis D, Magiorkinis G, Magiorkinis E, Ho SYW, Belshaw R, et al. (2013) Dating the origin and dispersal of hepatitis B virus infection in humans and primates. Hepatology 57: 908–916.
16. Liaw Y-F, Chu C-M, (2009) Hepatitis B virus infection. The Lancet 373: 582–592.
17. Gilbert C, Feschotte C, (2010) Genomic fossils calibrate the long-term evolution of hepadnaviruses. PLoS Biology 8: e1000495.
18. Cui J, Holmes EC, (2012) Endogenous hepadnaviruses in the genome of the budgerigar (Melopsittacus undulatus) and the evolution of avian hepadnaviruses. Journal of Virology 86: 7688–7691.
19. Liu W, Pan S, Yang H, Bai W, Shen Z, et al. (2012) The first full-length endogenous hepadnaviruses: identification and analysis. Journal of Virology 86: 9510–9513.
20. Chang S-F, Netter HJ, Hildt E, Schuster R, Schaefer S, et al. (2001) Duck hepatitis B virus expresses a regulatory HBx-like protein from a hidden open reading frame. Journal of Virology 75: 161–170.
21. Feitelson MA, Lee J, (2007) Hepatitis B virus integration, fragile sites, and hepatocarcinogenesis. Cancer Letters 252: 157–170.
22. Fourel G, Trepo C, Bougueleret L, Henglein B, Ponzetto A, et al. (1990) Frequent activation of N-myc genes by hepadnavirus insertion in woodchuck liver tumours. Nature 347: 294–298.
23. Fourel G, Couturier J, Wei Y, Apiou F, Tiollais P, et al. (1994) Evidence for long-range oncogene activation by hepadnavirus insertion. The EMBO Journal 13: 2526–2534.
24. Hansen LJ, Tennant BC, Seeger C, Ganem D, (1993) Differential activation of myc gene family members in hepatic carcinogenesis by closely related hepatitis B viruses. Molecular and Cellular Biology 13: 659–667.
25. Sung W-K, Zheng H, Li S, Chen R, Liu X, et al. (2012) Genome-wide survey of recurrent HBV integration in hepatocellular carcinoma. Nature Genetics 44: 765–769.
26. Wen Y, Golubkov VS, Strongin AY, Jiang W, Reed JC, (2008) Interaction of hepatitis B viral oncoprotein with cellular target HBXIP dysregulates centrosome dynamics and mitotic spindle formation. The Journal of Biological Chemistry 283: 2793–2803.
27. Shaffer HB, Minx P, Warren D, Shedlock A, Thomson R, et al. (2013) The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage. Genome Biology 14: R28.
28. Wang Z, Pascual-Anaya J, Zadissa A, Li W, Niimura Y, et al. (2013) The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan. Nature Genetics 45: 701–706.
29. Vonk FJ, Casewell NR, Henkel CV, Heimberg AM, Jansen HJ, et al. (2013) The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system. Proceedings of the National Academy of Sciences 110: 20651–20656.
30. Green RE, Braun EL, Armstrong J, Earl D, Nguyen N, et al. (2014) Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. Science 10.1126/science1254449 (in press).
31. Wan Q-H, Pan S-K, Hu L, Zhu Y, Xu P-W, et al. (2013) Genome analysis and signature discovery for diving and sensory properties of the endangered Chinese alligator. Cell Research 23: 1091–1105.
32. St John J, Braun E, Isberg S, Miles L, Chong A, et al. (2012) Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes. Genome Biology 13: 415.
33. Bradnam K, Fass J, Alexandrov A, Baranay P, Bechner M, et al. (2013) Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. GigaScience 2: 1–31.
34. Castoe TA, de Koning APJ, Hall KT, Card DC, Schield DR, et al. (2013) The Burmese python genome reveals the molecular basis for extreme adaptation in snakes. Proceedings of the National Academy of Sciences 110: 20645–20650.
35. Alföldi J, Di Palma F, Grabherr M, Williams C, Kong L, et al. (2011) The genome of the green anole lizard and a comparative analysis with birds and mammals. Nature 477: 587–591.
36. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, et al. (2001) Initial sequencing and analysis of the human genome. Nature 409: 860–921.
37. Mikkelsen TS, Wakefield MJ, Aken B, Amemiya CT, Chang JL, et al. (2007) Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature 447: 167–177.
38. Warren WC, Hillier LW, Graves JAM, Birney E, Ponting CP, et al. (2008) Genome analysis of the platypus reveals unique signatures of evolution. Nature 453: 175–183.
39. Shaffer HB (2009) Turtles (Testudines). In: Hedges SB, Kumar S, editors. The Timetree of Life. New York: Oxford University Press. pp. 398–401.
40. Shedlock AM, Edwards SV (2009) Amniotes (Amniota). In: Hedges SB, Kumar S, editors. The Timetree of Life. New York: Oxford University Press. pp. 375–379.
41. Harshman J, Huddleston CJ, Bollback JP, Parsons TJ, Braun MJ, (2003) True and false gharials: a nuclear gene phylogeny of Crocodylia. Systematic Biology 52: 386–402.
42. Brochu CA (2009) Crocodylians (Crocodylia). In: Hedges SB, Kumar S, editors. The Timetree of Life. New York: Oxford University Press. pp. 402–406.
43. Oaks JR, (2011) A time-calibrated species tree of Crocodylia reveals a recent radiation of the true crocodiles. Evolution 65: 3285–3297.
44. Janke A, Gullberg A, Hughes S, Aggarwal R, Arnason U, (2005) Mitogenomic analyses place the gharial (Gavialis gangeticus) on the crocodile tree and provide pre-K/T divergence times for most crocodilians. Journal of Molecular Evolution 61: 620–626.
45. Roos J, Aggarwal RK, Janke A, (2007) Extended mitogenomic phylogenetic analyses yield new insight into crocodylian evolution and their survival of the Cretaceous–Tertiary boundary. Molecular Phylogenetics and Evolution 45: 663–673.
46. Hugall AF, Foster R, Lee MSY, (2007) Calibration choice, rate smoothing, and the pattern of tetrapod diversification according to the long nuclear gene RAG-1. Systematic Biology 56: 543–563.
47. Pereira SL, Baker AJ, (2006) A mitogenomic timescale for birds detects variable phylogenetic rates of molecular evolution and refutes the standard molecular clock. Molecular Biology and Evolution 23: 1731–1740.
48. Okajima Y, Kumazawa Y, (2009) Mitogenomic perspectives into iguanid phylogeny and biogeography: Gondwanan vicariance for the origin of Madagascan oplurines. Gene 441: 28–35.
49. Rest JS, Ast JC, Austin CC, Waddell PJ, Tibbetts EA, et al. (2003) Molecular systematics of primary reptilian lineages and the tuatara mitochondrial genome. Molecular Phylogenetics and Evolution 29: 289–297.
50. Fujita P, Rhead B, Zweig A, Hinrichs A, Karolchik D, et al. (2011) The UCSC Genome Browser database: update 2011. Nucleic Acids Research 39: D876–D882.
51. Beck J, Nassal M, (2007) Hepatitis B virus replication. World Journal of Gastroenterology 13: 48–64.
52. Pollack JR, Ganem D, (1993) An RNA stem-loop structure directs hepatitis B virus genomic RNA encapsidation. Journal of Virology 67: 3254–3263.
53. Pollack JR, Ganem D, (1994) Site-specific RNA binding by a hepatitis B virus reverse transcriptase initiates two distinct reactions: RNA packaging and DNA synthesis. Journal of Virology 68: 5579–5587.
54. Nassal M, Rieger A, (1996) A bulged region of the hepatitis B virus RNA encapsidation signal contains the replication origin for discontinuous first-strand DNA synthesis. Journal of Virology 70: 2764–2773.
55. Beck J, Bartos H, Nassal M, (1997) Experimental Confirmation of a Hepatitis B Virus (HBV) ε-like Bulge-and-Loop Structure in Avian HBV RNA Encapsidation Signals. Virology 227: 500–504.
56. Piasecki T, Kurenbach B, Chrząstek K, Bednarek K, Kraberger S, et al. (2012) Molecular characterisation of an avihepadnavirus isolated from Psittacula krameri (ring-necked parrot). Archives of Virology 157: 585–590.
57. Bollyky P, Rambaut A, Harvey P, Holmes E, (1996) Recombination between sequences of hepatitis B virus from different genotypes. Journal of Molecular Evolution 42: 97–102.
58. Meier P, Scougall CA, Will H, Burrell CJ, Jilbert AR, (2003) A duck hepatitis B virus strain with a knockout mutation in the putative X ORF shows similar infectivity and in vivo growth characteristics to wild-type virus. Virology 317: 291–298.
59. Keese PK, Gibbs A, (1992) Origins of genes: “big bang” or continuous creation? Proceedings of the National Academy of Sciences 89: 9489–9493.
60. Pavesi A, Magiorkinis G, Karlin DG, (2013) Viral proteins originated de novo by overprinting can be identified by codon usage: application to the “gene nursery” of Deltaretroviruses. PLoS Computational Biology 9: e1003162.
61. Krakauer DC, (2000) Stability and evolution of overlapping genes. Evolution 54: 731–739.
62. Tollis M, Boissinot S, (2011) The transposable element profile of the Anolis genome: How a lizard can provide insights into the evolution of vertebrate genome size and structure. Mobile Genetic Elements 1: 107–111.
63. Suh A, Churakov G, Ramakodi MP, Platt II RN, Jurka J, et al. (2014) Multiple lineages of ancient CR1 retroposons shaped the early genome evolution of amniotes. Genome Biology and Evolution 10.1093/gbe/evu256 (in press).
64. Braun E, Kimball R, Han K-L, Iuhasz-Velez N, Bonilla A, et al. (2011) Homoplastic microinversions and the avian tree of life. BMC Evolutionary Biology 11: 141.
65. Schuster R, Hildt E, Chang S-F, Terradillos O, Pollicino T, et al. (2002) Conserved transactivating and pro-apoptotic functions of hepadnaviral X protein in ortho- and avihepadnaviruses. Oncogene 21: 6606–6613.
66. van Hemert FJ, van de Klundert MAA, Lukashov VV, Kootstra NA, Berkhout B, et al. (2011) Protein X of hepatitis B virus: origin and structure similarity with the central domain of DNA glycosylase. PLoS ONE 6: e23392.
67. Li T, Robert EI, van Breugel PC, Strubin M, Zheng N, (2010) A promiscuous α-helical motif anchors viral hijackers and substrate receptors to the CUL4–DDB1 ubiquitin ligase machinery. Nature Structural & Molecular Biology 17: 105–112.
68. Lin W-S, Jiao B-Y, Wu Y-L, Chen W-N, Lin X, (2012) Hepatitis B virus X protein blocks filamentous actin bundles by interaction with eukaryotic translation elongation factor 1 alpha 1. Journal of Medical Virology 84: 871–877.
69. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research 25: 3389–3402.
70. Katoh K, Toh H, (2008) Recent developments in the MAFFT multiple sequence alignment program. Briefings in Bioinformatics 9: 286–298.
71. Suh A, Paus M, Kiefmann M, Churakov G, Franke FA, et al. (2011) Mesozoic retroposons reveal parrots as the closest living relatives of passerine birds. Nature Communications 2: 443.
72. Yang Z, (2007) PAML 4: Phylogenetic analysis by maximum likelihood. Molecular Biology and Evolution 24: 1586–1591.
73. Darriba D, Taboada GL, Doallo R, Posada D, (2012) jModelTest 2: more models, new heuristics and parallel computing. Nat Meth 9: 772–772.
74. Zuker M, (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Research 31: 3406–3415.
75. Zlotnick A, Stahl SJ, Wingfield PT, Conway JF, Cheng N, et al. (1998) Shared motifs of the capsid proteins of hepadnaviruses and retroviruses suggest a common evolutionary origin. FEBS Letters 431: 301–304.
76. Stamatakis A, Hoover P, Rougemont J, (2008) A rapid bootstrap algorithm for the RAxML web servers. Systematic Biology 75: 758–771.
77. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution 28: 2731–2739.
78. Hedges SB, Vidal N (2009) Lizards, snakes, and amphisbaenians (Squamata). In: Hedges SB, Kumar S, editors. The Timetree of Life. New York: Oxford University Press. pp. 383–389.
79. Vidal N, Rage J-C, Couloux A, Hedges SB (2009) Snakes (Serpentes). In: Hedges SB, Kumar S, editors. The Timetree of Life. New York: Oxford University Press. pp. 390–397.
80. Brown JW, van Tuinen M (2011) Evolving perceptions on the antiquity of the modern avian tree. In: Dyke G, Kaiser G, editors. Living Dinosaurs: The Evolutionary History of Modern Birds. Chichester: John Wiley & Sons, Ltd. pp. 306–324.