Evolutionary studies on the betaretrovirus RERV-H in the Leporidae family reveal an endogenization in the ancestor of Oryctolagus, Bunolagus and Pentalagus at 9 million years ago
Tài liệu tham khảo
Abrantes, 2011, A shared unusual genetic change at the chemokine receptor type 5 between Oryctolagus, Bunolagus and Pentalagus, Conserv. Genet., 12, 325, 10.1007/s10592-009-9990-1
Andersson, 1998, Retroelements in the human MHC class II region, Trends Genet., 14, 109, 10.1016/S0168-9525(97)01359-0
Boeke, 1997, Retrotransposons, endogenous retroviruses, and the evolution of retroelements
Carmo, 2006, Genetic variation at chemokine receptor CCR5 in leporids: alteration at the 2nd extracellular domain by gene conversion with CCR2 in Oryctolagus, but not in Sylvilagus and Lepus species, Immunogenetics, 58, 494, 10.1007/s00251-006-0095-4
Chuong, 2016, Regulatory evolution of innate immunity through co-option of endogenous retroviruses, Science, 351, 1083, 10.1126/science.aad5497
Dimmic, 2002, rtREV: an amino acid substitution matrix for inference of retrovirus and reverse transcriptase phylogeny, J. Mol. Evol., 55, 65, 10.1007/s00239-001-2304-y
Feschotte, 2012, Endogenous viruses: insights into viral evolution and impact on host biology, Nat. Rev. Genet., 13, 283, 10.1038/nrg3199
Fletcher, 2010, Hare TRIM5alpha restricts divergent retroviruses and exhibits significant sequence variation from closely related lagomorpha TRIM5 genes, J. Virol., 84, 12463, 10.1128/JVI.01514-10
Forsman, 2003, Uptake of amplifiable fragments of retrotransposon DNA from the human alimentary tract, Mol. Genet. Genom., 270, 362, 10.1007/s00438-003-0930-3
Forsman, 2003, Single-tube nested quantitative PCR: a rational and sensitive technique for detection of retroviral DNA. Application to RERV-H/HRV-5 and confirmation of its rabbit origin, J. Virol. Methods, 111, 1, 10.1016/S0166-0934(03)00127-7
Griffiths, 1997, A novel exogenous retrovirus sequence identified in humans, J. Virol., 71, 2866, 10.1128/jvi.71.4.2866-2872.1997
Griffiths, 2002, Novel endogenous retrovirus in rabbits previously reported as human retrovirus 5, J. Virol., 76, 7094, 10.1128/JVI.76.14.7094-7102.2002
Hall, 1999, BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT, Nucleic Acids Symp. Ser., 41, 95
Jern, 2008, Effects of retroviruses on host genome function, Annu. Rev. Genet., 42, 709, 10.1146/annurev.genet.42.110807.091501
Katzourakis, 2007, Discovery and analysis of the first endogenous lentivirus, Proc. Natl. Acad. Sci. U. S. A., 104, 6261, 10.1073/pnas.0700471104
Kearse, 2012, Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data, Bioinformatics, 28, 1647, 10.1093/bioinformatics/bts199
Keckesova, 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, 7, 10.1016/j.virol.2008.10.045
Kumar, 2016, MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets, Mol. Biol. Evol., 33, 1870, 10.1093/molbev/msw054
Lemos de Matos, 2015, Endogenization of mouse mammary tumor virus (MMTV)-like elements in genomes of pikas (Ochotona sp.), Virus Res., 210, 22, 10.1016/j.virusres.2015.06.021
Llorens, 2011, The Gypsy Database (GyDB) of mobile genetic elements: release 2. 0, Nucleic Acids Res., 39, D70, 10.1093/nar/gkq1061
Matthee, 2004, A molecular supermatrix of the rabbits and hares (Leporidae) allows for the identification of five intercontinental exchanges during the Miocene, Syst. Biol., 53, 433, 10.1080/10635150490445715
Melo-Ferreira, 2015, The phylogeny of pikas (Ochotona) inferred from a multilocus coalescent approach, Mol. Phylogenet. Evol., 84, 240, 10.1016/j.ympev.2015.01.004
Mourier, 2015, Characterizing novel endogenous retroviruses from genetic variation inferred from short sequence reads, Sci. Rep., 5, 15644, 10.1038/srep15644
Neves, 2015, Evolutionary insights into IL17A in lagomorphs, Mediators Inflamm., 2015, 367670, 10.1155/2015/367670
Neves, 2015, Genetic characterization of interleukins (IL-1alpha, IL-1beta, IL-2, IL-4, IL-8, IL-10, IL-12A, IL-12B, IL-15 and IL-18) with relevant biological roles in lagomorphs, Innate Immun., 21, 787, 10.1177/1753425915606209
Neves, 2016, Evolution of CCL11: genetic characterization in lagomorphs and evidence of positive and purifying selection in mammals, Innate Immun., 22, 336, 10.1177/1753425916647471
Pinheiro, 2016, An overview of the lagomorph immune system and its genetic diversity, Immunogenetics, 68, 83, 10.1007/s00251-015-0868-8
Robinson, 2005, Phylogeny and evolutionary origins of the Leporidae: a review of cytogenetics, molecular analyses and a supermatrix analysis, Mamm. Rev., 35, 231, 10.1111/j.1365-2907.2005.00073.x
Tamura, 2004, Prospects for inferring very large phylogenies by using the neighbor-joining method, Proc. Natl. Acad. Sci. U. S. A., 101, 11030, 10.1073/pnas.0404206101
Thompson, 1994, CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice, Nucleic Acids Res., 22, 4673, 10.1093/nar/22.22.4673
Voisset, 2003, Rabbit endogenous retrovirus-H encodes a functional protease, J. Gen. Virol., 84, 215, 10.1099/vir.0.18670-0
Yap, 2013, Apparent effect of rabbit endogenous lentivirus type K acquisition on retrovirus restriction by lagomorph Trim5alphas, Philos. Trans. Royal Soc. Lond. B Biol. Sci, 368, 20120498, 10.1098/rstb.2012.0498
de Matos, 2011, Study of Sylvilagus rabbit TRIM5alpha species-specific domain: how ancient endoviruses could have shaped the antiviral repertoire in Lagomorpha, BMC Evol. Biol., 11, 294, 10.1186/1471-2148-11-294
van der Loo, 2009, Sharing of endogenous lentiviral gene fragments among leporid lineages separated for more than 12 million years, J. Virol., 83, 2386, 10.1128/JVI.01116-08
van der Loo, 2012, Pseudogenization of the MCP-2/CCL8 chemokine gene in European rabbit (genus Oryctolagus), but not in species of Cottontail rabbit (Sylvilagus) and Hare (Lepus), BMC Genet., 13, 72, 10.1186/1471-2156-13-72
van der Loo, 2016, Adaptive gene loss? tracing back the pseudogenization of the rabbit CCL8 chemokine, J. Mol. Evol., 83, 12, 10.1007/s00239-016-9747-7