메뉴 건너뛰기




Volumn 110, Issue 50, 2013, Pages 20146-20151

Broad-scale phylogenomics provides insights into retrovirus - Host evolution

Author keywords

[No Author keywords available]

Indexed keywords

ARMADILLO; ARTICLE; BAT; BIRD; COMPUTER MODEL; ENDOGENOUS RETROVIRUS; GENOME; GIBBON LEUKEMIA VIRUS; HEDGEHOG; HOST; MOLECULAR CLOCK; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; OPOSSUM; PHYLOGENETIC TREE; PHYLOGENOMICS; PRIORITY JOURNAL; RAT; RETICULOENDOTHELIOSIS VIRUS; RETROVIRUS; RETROVIRUS INFECTION; SPECIES; VERTEBRATE;

EID: 84890276747     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1315419110     Document Type: Article
Times cited : (86)

References (48)
  • 1
    • 58149507192 scopus 로고    scopus 로고
    • Effects of retroviruses on host genome function
    • Jern P, Coffin JM (2008) Effects of retroviruses on host genome function. Annu Rev Genet 42:709-732.
    • (2008) Annu Rev Genet , vol.42 , pp. 709-732
    • Jern, P.1    Coffin, J.M.2
  • 2
    • 84861188188 scopus 로고    scopus 로고
    • Studies of endogenous retroviruses reveal a continuing evolutionary saga
    • Stoye JP (2012) Studies of endogenous retroviruses reveal a continuing evolutionary saga. Nat Rev Microbiol 10(6):395-406.
    • (2012) Nat Rev Microbiol , vol.10 , Issue.6 , pp. 395-406
    • Stoye, J.P.1
  • 4
    • 27344432183 scopus 로고    scopus 로고
    • Use of endogenous retroviral sequences (ERVs) and structural markers for retroviral phylogenetic inference and taxonomy
    • Jern P, Sperber GO, Blomberg J (2005) Use of endogenous retroviral sequences (ERVs) and structural markers for retroviral phylogenetic inference and taxonomy. Retrovirology 2:50.
    • (2005) Retrovirology , vol.2 , pp. 50
    • Jern, P.1    Sperber, G.O.2    Blomberg, J.3
  • 5
    • 84858429240 scopus 로고    scopus 로고
    • Endogenous viruses: Insights into viral evolution and impact on host biology
    • Feschotte C, Gilbert C (2012) Endogenous viruses: Insights into viral evolution and impact on host biology. Nat Rev Genet 13(4):283-296.
    • (2012) Nat Rev Genet , vol.13 , Issue.4 , pp. 283-296
    • Feschotte, C.1    Gilbert, C.2
  • 6
    • 0001602245 scopus 로고    scopus 로고
    • Retroviral pathogenesis
    • eds Coffin JM, Hughes SH, Varmus HE (Cold Spring Harbor Lab Press, Cold Spring Harbor, NY)
    • Rosenberg N, Jolicoeur P (1997) Retroviral pathogenesis. Retroviruses, eds Coffin JM, Hughes SH, Varmus HE (Cold Spring Harbor Lab Press, Cold Spring Harbor, NY), pp 475-586.
    • (1997) Retroviruses , pp. 475-586
    • Rosenberg, N.1    Jolicoeur, P.2
  • 7
    • 0033049550 scopus 로고    scopus 로고
    • Interclass transmission and phyletic host tracking in murine leukemia virus-related retroviruses
    • Martin J, Herniou E, Cook J, O'Neill RW, Tristem M (1999) Interclass transmission and phyletic host tracking in murine leukemia virus-related retroviruses. J Virol 73(3):2442-2449.
    • (1999) J Virol , vol.73 , Issue.3 , pp. 2442-2449
    • Martin, J.1    Herniou, E.2    Cook, J.3    O'Neill, R.W.4    Tristem, M.5
  • 8
    • 0034004490 scopus 로고    scopus 로고
    • The nucleotide sequence of koala (Phascolarctos cinereus) retrovirus: A novel type C endogenous virus related to Gibbon ape leukemia virus
    • Hanger JJ, Bromham LD, McKee JJ, O'Brien TM, Robinson WF (2000) The nucleotide sequence of koala (Phascolarctos cinereus) retrovirus: A novel type C endogenous virus related to Gibbon ape leukemia virus. J Virol 74(9):4264-4272.
    • (2000) J Virol , vol.74 , Issue.9 , pp. 4264-4272
    • Hanger, J.J.1    Bromham, L.D.2    McKee, J.J.3    O'Brien, T.M.4    Robinson, W.F.5
  • 9
    • 84869003221 scopus 로고    scopus 로고
    • Analyses of pig genomes provide insight into porcine demography and evolution
    • Groenen MAM, et al. (2012) Analyses of pig genomes provide insight into porcine demography and evolution. Nature 491(7424):393-398.
    • (2012) Nature , vol.491 , Issue.7424 , pp. 393-398
    • Groenen, M.A.M.1
  • 10
    • 84855858621 scopus 로고    scopus 로고
    • Characterization, mapping, and distribution of the two XMRV parental proviruses
    • Cingöz O, et al. (2012) Characterization, mapping, and distribution of the two XMRV parental proviruses. J Virol 86(1):328-338.
    • (2012) J Virol , vol.86 , Issue.1 , pp. 328-338
    • Cingöz, O.1
  • 11
    • 33646721361 scopus 로고    scopus 로고
    • Transspecies transmission of the endogenous koala retrovirus
    • Fiebig U, Hartmann MG, Bannert N, Kurth R, Denner J (2006) Transspecies transmission of the endogenous koala retrovirus. J Virol 80(11):5651-5654.
    • (2006) J Virol , vol.80 , Issue.11 , pp. 5651-5654
    • Fiebig, U.1    Hartmann, M.G.2    Bannert, N.3    Kurth, R.4    Denner, J.5
  • 13
    • 0031054438 scopus 로고    scopus 로고
    • Infection of human cells by an endogenous retrovirus of pigs
    • Patience C, Takeuchi Y, Weiss RA (1997) Infection of human cells by an endogenous retrovirus of pigs. Nat Med 3(3):282-286.
    • (1997) Nat Med , vol.3 , Issue.3 , pp. 282-286
    • Patience, C.1    Takeuchi, Y.2    Weiss, R.A.3
  • 14
    • 34548590461 scopus 로고    scopus 로고
    • Automated recognition of retroviral sequences in genomic data - RetroTector
    • Sperber GO, Airola T, Jern P, Blomberg J (2007) Automated recognition of retroviral sequences in genomic data - RetroTector. Nucleic Acids Res 35(15):4964-4976.
    • (2007) Nucleic Acids Res , vol.35 , Issue.15 , pp. 4964-4976
    • Sperber, G.O.1    Airola, T.2    Jern, P.3    Blomberg, J.4
  • 15
    • 40849097775 scopus 로고    scopus 로고
    • Rates of evolutionary change in viruses: Patterns and determinants
    • Duffy S, Shackelton LA, Holmes EC (2008) Rates of evolutionary change in viruses: Patterns and determinants. Nat Rev Genet 9(4):267-276.
    • (2008) Nat Rev Genet , vol.9 , Issue.4 , pp. 267-276
    • Duffy, S.1    Shackelton, L.A.2    Holmes, E.C.3
  • 16
    • 84879977879 scopus 로고    scopus 로고
    • An exogenous retrovirus isolated from koalas with malignant neoplasias in a US zoo
    • Xu W, et al. (2013) An exogenous retrovirus isolated from koalas with malignant neoplasias in a US zoo. Proc Natl Acad Sci USA 110(28):11547-11552.
    • (2013) Proc Natl Acad Sci USA , vol.110 , Issue.28 , pp. 11547-11552
    • Xu, W.1
  • 17
    • 33745972414 scopus 로고    scopus 로고
    • Retroviral invasion of the koala genome
    • Tarlinton RE, Meers J, Young PR (2006) Retroviral invasion of the koala genome. Nature 442(7098):79-81.
    • (2006) Nature , vol.442 , Issue.7098 , pp. 79-81
    • Tarlinton, R.E.1    Meers, J.2    Young, P.R.3
  • 18
    • 84879324277 scopus 로고    scopus 로고
    • One hundred twenty years of koala retrovirus evolution determined from museum skins
    • Ávila-Arcos MC, et al. (2013) One hundred twenty years of koala retrovirus evolution determined from museum skins. Mol Biol Evol 30(2):299-304.
    • (2013) Mol Biol Evol , vol.30 , Issue.2 , pp. 299-304
    • Ávila-Arcos, M.C.1
  • 19
    • 0032766857 scopus 로고    scopus 로고
    • Multiple comparisons of log-likelihoods with applications to phylogenetic inference
    • Shimodaira H, Hasegawa M (1999) Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol Biol Evol 16(8):1114-1116.
    • (1999) Mol Biol Evol , vol.16 , Issue.8 , pp. 1114-1116
    • Shimodaira, H.1    Hasegawa, M.2
  • 20
    • 84883170936 scopus 로고    scopus 로고
    • The extraordinary evolutionary history of the reticuloendotheliosis viruses
    • Niewiadomska AM, Gifford RJ (2013) The extraordinary evolutionary history of the reticuloendotheliosis viruses. PLoS Biol 11(8):e1001642.
    • (2013) PLoS Biol , vol.11 , Issue.8
    • Niewiadomska, A.M.1    Gifford, R.J.2
  • 21
    • 84865124450 scopus 로고    scopus 로고
    • Identification of diverse groups of endogenous gammaretroviruses in mega- and microbats
    • Cui J, et al. (2012) Identification of diverse groups of endogenous gammaretroviruses in mega- and microbats. J Gen Virol 93(Pt 9):2037-2045.
    • (2012) J Gen Virol , vol.93 , Issue.PART 9 , pp. 2037-2045
    • Cui, J.1
  • 22
    • 84858792076 scopus 로고    scopus 로고
    • Behavioral, ecological, and evolutionary aspects of meateating by Sumatran orangutans (Pongo abelii)
    • Hardus ME, et al. (2012) Behavioral, ecological, and evolutionary aspects of meateating by Sumatran orangutans (Pongo abelii). Int J Primatol 33(2):287-304.
    • (2012) Int J Primatol , vol.33 , Issue.2 , pp. 287-304
    • Hardus, M.E.1
  • 23
    • 77949733453 scopus 로고    scopus 로고
    • Vertebrate DNA in fecal samples from bonobos and gorillas: Evidence for meat consumption or artefact?
    • Hofreiter M, Kreuz E, Eriksson J, Schubert G, Hohmann G (2010) Vertebrate DNA in fecal samples from bonobos and gorillas: Evidence for meat consumption or artefact? PLoS ONE 5(2):e9419.
    • (2010) PLoS ONE , vol.5 , Issue.2
    • Hofreiter, M.1    Kreuz, E.2    Eriksson, J.3    Schubert, G.4    Hohmann, G.5
  • 25
    • 80355129314 scopus 로고    scopus 로고
    • Multiple geographic origins of commensalism and complex dispersal history of Black Rats
    • Aplin KP, et al. (2011) Multiple geographic origins of commensalism and complex dispersal history of Black Rats. PLoS ONE 6(11):e26357.
    • (2011) PLoS ONE , vol.6 , Issue.11
    • Aplin, K.P.1
  • 26
    • 72849122986 scopus 로고    scopus 로고
    • Molecular characterization of a novel gammaretrovirus in killer whales (Orcinus orca)
    • Lamere SA, et al. (2009) Molecular characterization of a novel gammaretrovirus in killer whales (Orcinus orca). J Virol 83(24):12956-12967.
    • (2009) J Virol , vol.83 , Issue.24 , pp. 12956-12967
    • Lamere, S.A.1
  • 27
    • 84877597071 scopus 로고    scopus 로고
    • Ancient invasion of an extinct gammaretrovirus in cetaceans
    • Wang L, et al. (2013) Ancient invasion of an extinct gammaretrovirus in cetaceans. Virology 441(1):66-69.
    • (2013) Virology , vol.441 , Issue.1 , pp. 66-69
    • Wang, L.1
  • 28
    • 0343117821 scopus 로고
    • Isolation from the Asian mouse Mus caroli of an endogenous type C virus related to infectious primate type C viruses
    • Lieber MM, et al. (1975) Isolation from the Asian mouse Mus caroli of an endogenous type C virus related to infectious primate type C viruses. Proc Natl Acad Sci USA 72(6):2315-2319.
    • (1975) Proc Natl Acad Sci USA , vol.72 , Issue.6 , pp. 2315-2319
    • Lieber, M.M.1
  • 29
    • 84898673851 scopus 로고    scopus 로고
    • On the concept and elucidation of endogenous retroviruses
    • Weiss RA (2013) On the concept and elucidation of endogenous retroviruses. Philos Trans R Soc Lond B Biol Sci 368(1626):20120494.
    • (2013) Philos Trans R Soc Lond B Biol Sci , vol.368 , Issue.1626 , pp. 20120494
    • Weiss, R.A.1
  • 30
    • 84883304227 scopus 로고    scopus 로고
    • The avian XPR1 gammaretrovirus receptor is under positive selection and is disabled in bird species in contact with virus-infected wild mice
    • Martin C, Buckler-White A, Wollenberg K, Kozak CA (2013) The avian XPR1 gammaretrovirus receptor is under positive selection and is disabled in bird species in contact with virus-infected wild mice. J Virol 87(18):10094-10104.
    • (2013) J Virol , vol.87 , Issue.18 , pp. 10094-10104
    • Martin, C.1    Buckler-White, A.2    Wollenberg, K.3    Kozak, C.A.4
  • 31
    • 77956477507 scopus 로고    scopus 로고
    • The evolution of HIV-1 and the origin of AIDS
    • Sharp PM, Hahn BH (2010) The evolution of HIV-1 and the origin of AIDS. Philos Trans R Soc Lond B Biol Sci 365(1552):2487-2494.
    • (2010) Philos Trans R Soc Lond B Biol Sci , vol.365 , Issue.1552 , pp. 2487-2494
    • Sharp, P.M.1    Hahn, B.H.2
  • 32
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: Multiple sequence alignment with high accuracy and high throughput
    • Edgar RC (2004) MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32(5):1792-1797.
    • (2004) Nucleic Acids Res , vol.32 , Issue.5 , pp. 1792-1797
    • Edgar, R.C.1
  • 33
    • 67650757433 scopus 로고    scopus 로고
    • trimAl: A tool for automated alignment trimming in large-scale phylogenetic analyses
    • Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T (2009) trimAl: A tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25(15):1972-1973.
    • (2009) Bioinformatics , vol.25 , Issue.15 , pp. 1972-1973
    • Capella-Gutiérrez, S.1    Silla-Martínez, J.M.2    Gabaldón, T.3
  • 34
    • 80052006478 scopus 로고    scopus 로고
    • Missing data in phylogenetic analysis: Reconciling results from simulations and empirical data
    • Wiens JJ, Morrill MC (2011) Missing data in phylogenetic analysis: Reconciling results from simulations and empirical data. Syst Biol 60(5):719-731.
    • (2011) Syst Biol , vol.60 , Issue.5 , pp. 719-731
    • Wiens, J.J.1    Morrill, M.C.2
  • 35
    • 84858080561 scopus 로고    scopus 로고
    • Misleading results of likelihood-based phylogenetic analyses in the presence of missing data
    • Simmons MP (2012) Misleading results of likelihood-based phylogenetic analyses in the presence of missing data. Cladistics 28(2):208-222.
    • (2012) Cladistics , vol.28 , Issue.2 , pp. 208-222
    • Simmons, M.P.1
  • 36
    • 33845296602 scopus 로고    scopus 로고
    • Identification of an infectious progenitor for the multiplecopy HERV-K human endogenous retroelements
    • Dewannieux M, et al. (2006) Identification of an infectious progenitor for the multiplecopy HERV-K human endogenous retroelements. Genome Res 16(12):1548-1556.
    • (2006) Genome Res , vol.16 , Issue.12 , pp. 1548-1556
    • Dewannieux, M.1
  • 37
    • 18144390153 scopus 로고    scopus 로고
    • Sequence variability, gene structure, and expression of full-length human endogenous retrovirus H
    • Jern P, Sperber GO, Ahlsén G, Blomberg J (2005) Sequence variability, gene structure, and expression of full-length human endogenous retrovirus H. J Virol 79(10):6325-6337.
    • (2005) J Virol , vol.79 , Issue.10 , pp. 6325-6337
    • Jern, P.1    Sperber, G.O.2    Ahlsén, G.3    Blomberg, J.4
  • 39
    • 58749086368 scopus 로고    scopus 로고
    • Identification of a RELIK orthologue in the European hare (Lepus europaeus) reveals a minimum age of 12 million years for the lagomorph lentiviruses
    • Keckesova Z, Ylinen LM, Towers GJ, Gifford RJ, Katzourakis A (2009) Identification of a RELIK orthologue in the European hare (Lepus europaeus) reveals a minimum age of 12 million years for the lagomorph lentiviruses. Virology 384(1):7-11.
    • (2009) Virology , vol.384 , Issue.1 , pp. 7-11
    • Keckesova, Z.1    Ylinen, L.M.2    Towers, G.J.3    Gifford, R.J.4    Katzourakis, A.5
  • 40
    • 35948967657 scopus 로고    scopus 로고
    • Role of APOBEC3 in genetic diversity among endogenous murine leukemia viruses
    • Jern P, Stoye JP, Coffin JM (2007) Role of APOBEC3 in genetic diversity among endogenous murine leukemia viruses. PLoS Genet 3(10):2014-2022.
    • (2007) PLoS Genet , vol.3 , Issue.10 , pp. 2014-2022
    • Jern, P.1    Stoye, J.P.2    Coffin, J.M.3
  • 42
    • 33750403801 scopus 로고    scopus 로고
    • RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
    • Stamatakis A (2006) RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22(21):2688-2690.
    • (2006) Bioinformatics , vol.22 , Issue.21 , pp. 2688-2690
    • Stamatakis, A.1
  • 44
    • 77949718257 scopus 로고    scopus 로고
    • FastTree 2 - Approximately maximum-likelihood trees for large alignments
    • Price MN, Dehal PS, Arkin AP (2010) FastTree 2 - approximately maximum-likelihood trees for large alignments. PLoS ONE 5(3):e9490.
    • (2010) PLoS ONE , vol.5 , Issue.3
    • Price, M.N.1    Dehal, P.S.2    Arkin, A.P.3
  • 45
    • 0041386108 scopus 로고    scopus 로고
    • MrBayes 3: Bayesian phylogenetic inference under mixed models
    • Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19(12):1572-1574.
    • (2003) Bioinformatics , vol.19 , Issue.12 , pp. 1572-1574
    • Ronquist, F.1    Huelsenbeck, J.P.2
  • 46
    • 84865382153 scopus 로고    scopus 로고
    • More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs
    • Crawford NG, et al. (2012) More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs. Biol Lett 8(5):783-786.
    • (2012) Biol Lett , vol.8 , Issue.5 , pp. 783-786
    • Crawford, N.G.1
  • 47
    • 80055070300 scopus 로고    scopus 로고
    • Impacts of the Cretaceous Terrestrial Revolution and KPg extinction on mammal diversification
    • Meredith RW, et al. (2011) Impacts of the Cretaceous Terrestrial Revolution and KPg extinction on mammal diversification. Science 334(6055):521-524.
    • (2011) Science , vol.334 , Issue.6055 , pp. 521-524
    • Meredith, R.W.1
  • 48
    • 77952854165 scopus 로고    scopus 로고
    • Genome-wide synteny through highly sensitive sequence alignment: Satsuma
    • Grabherr MG, et al. (2010) Genome-wide synteny through highly sensitive sequence alignment: Satsuma. Bioinformatics 26(9):1145-1151.
    • (2010) Bioinformatics , vol.26 , Issue.9 , pp. 1145-1151
    • Grabherr, M.G.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.