Azzam O, Chancellor TCB. The biology, epidemiology, and management of rice tungro disease in Asia. Plant Dis. 2002;86:88–100.
Article
PubMed
CAS
Google Scholar
Bombarely A, Moser M, Amrad A, Bao M, Bapaume L, Barry CS, et al. Insight into the evolution of the Solanaceae from the parental genomes of Petunia hybrida. Nat Plants. 2016;2:16074.
Article
PubMed
CAS
Google Scholar
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, et al. BLAST+: architecture and applications. BMC Bioinformatics. 2009;10:421.
Article
PubMed
PubMed Central
Google Scholar
Capella-Gutierrez S, Silla-Martinez JM, Gabaldon T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics. 2009;25:1972–3.
Article
PubMed
PubMed Central
CAS
Google Scholar
Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol. 2000;17:540–52.
Article
PubMed
CAS
Google Scholar
Chabannes M, Baurens FC, Duroy PO, Bocs S, Vernerey MS, Rodier-Goud M, et al. Three infectious viral species lying in wait in the banana genome. J Virol. 2013;87:8624–37.
Article
PubMed
PubMed Central
CAS
Google Scholar
Diop SI, Geering ADW, Alfama-Depauw F, Loaec M, Teycheney PY, Maumus F. Tracheophyte genomes keep track of the deep evolution of the Caulimoviridae. Sci Rep. 2018;8:572.
Article
PubMed
PubMed Central
Google Scholar
Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32:1792–7.
Article
PubMed
PubMed Central
CAS
Google Scholar
Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010;26:2460–1.
Article
PubMed
CAS
Google Scholar
Edgar RC, Myers EW. PILER: identification and classification of genomic repeats. Bioinformatics. 2005;21(Suppl 1):i152–8.
Article
PubMed
CAS
Google Scholar
Flutre T, Duprat E, Feuillet C, Quesneville H. Considering transposable element diversification in de novo annotation approaches. PLoS One. 2011;6:e16526.
Article
PubMed
PubMed Central
CAS
Google Scholar
Geering AD, 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.
Article
PubMed
CAS
Google Scholar
Geering ADW. Caulimoviridae (plant Pararetroviruses). In: eLS. Hoboken: Wiley; 2019. p. 1–11.
Google Scholar
Geijskes RJ, Braithwaite KS, Smith GR, Dale JL, Harding RM. Sugarcane bacilliform virus encapsidates genome concatamers and does not appear to integrate into the Saccharum officinarum genome. Arch Virol. 2004;149:791–8.
Article
PubMed
CAS
Google Scholar
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;59:307–21.
Article
PubMed
CAS
Google Scholar
Hoede C, Arnoux S, Moisset M, Chaumier T, Inizan O, Jamilloux V, et al. PASTEC: an automatic transposable element classification tool. PLoS One. 2014;9:e91929.
Article
PubMed
PubMed Central
Google Scholar
Hull R, Covey SN. Retroelements: propagation and adaptation. Virus Genes. 1995;11:105–18.
Article
PubMed
CAS
Google Scholar
Jaillon O, Aury JM, Noel B, Policriti A, Clepet C, Casagrande A, et al. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature. 2007;449:463–7.
Article
PubMed
CAS
Google Scholar
Jakowitsch J, Mette MF, van Der Winden J, Matzke MA, Matzke AJ. Integrated pararetroviral sequences define a unique class of dispersed repetitive DNA in plants. Proc Natl Acad Sci U S A. 1999;96:13241–6.
Article
PubMed
PubMed Central
CAS
Google Scholar
Kim S, Park M, Yeom SI, Kim YM, Lee JM, Lee HA, et al. Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species. Nat Genet. 2014;46:270–8.
Article
PubMed
CAS
Google Scholar
Krupovic M, Blomberg J, Coffin JM, Dasgupta I, Fan H, Geering AD, et al. Ortervirales: new virus order unifying five families of reverse-transcribing viruses. J Virol. 2018;92(12):e00515–8.
Article
PubMed
PubMed Central
CAS
Google Scholar
Liu R, Koyanagi KO, Chen S, Kishima Y. Evolutionary force of AT-rich repeats to trap genomic and episomal DNAs into the rice genome: lessons from endogenous pararetrovirus. Plant J. 2012;72:817–28.
Article
PubMed
CAS
Google Scholar
Llorens C, Futami R, Covelli L, Dominguez-Escriba L, Viu JM, Tamarit D, et al. The Gypsy Database (GyDB) of mobile genetic elements: release 2.0. Nucleic Acids Res. 2011;39:D70–4.
Article
PubMed
CAS
Google Scholar
Llorens C, Soriano B, Krupovic M, Ictv Report, C. ICTV virus taxonomy profile: metaviridae. J Gen Virol. 2020;101:1131–2.
Article
PubMed
PubMed Central
CAS
Google Scholar
Llorens C, Soriano B, Krupovic M, Ictv Report, C. ICTV virus taxonomy profile: Pseudoviridae. J Gen Virol. 2021;102(3):001563.
Article
PubMed
PubMed Central
CAS
Google Scholar
Lu S, Wang J, Chitsaz F, Derbyshire MK, Geer RC, Gonzales NR, et al. CDD/SPARCLE: the conserved domain database in 2020. Nucleic Acids Res. 2020;48:D265–8.
Article
PubMed
CAS
Google Scholar
Martiniere A, Bak A, Macia JL, Lautredou N, Gargani D, Doumayrou J, et al. A virus responds instantly to the presence of the vector on the host and forms transmission morphs. Elife. 2013;2:e00183.
Article
PubMed
PubMed Central
Google Scholar
Merkel D. Docker: lightweight linux containers for consistent development and deployment. Linux J. 2014;239:2.
Google Scholar
Price AL, Jones NC, Pevzner PA. De novo identification of repeat families in large genomes. Bioinformatics. 2005;21(Suppl 1):i351–8.
Article
PubMed
CAS
Google Scholar
Quesneville H, Nouaud D, Anxolabehere D. Detection of new transposable element families in Drosophila melanogaster and Anopheles gambiae genomes. J Mol Evol. 2003;57(Suppl 1):S50–9.
Article
PubMed
CAS
Google Scholar
Richert-Poggeler KR, Vijverberg K, Alisawi O, Chofong GN, Heslop-Harrison JSP, Schwarzacher T. Participation of multifunctional RNA in replication, recombination and regulation of endogenous plant pararetroviruses (EPRVs). Front Plant Sci. 2021;12:689307.
Article
PubMed
PubMed Central
Google Scholar
Schmidt N, Seibt KM, Weber B, Schwarzacher T, Schmidt T, Heitkam T. Broken, silent, and in hiding: tamed endogenous pararetroviruses escape elimination from the genome of sugar beet (Beta vulgaris). Ann Bot. 2021;128:281–99.
Article
PubMed
PubMed Central
CAS
Google Scholar
Serfraz S, Sharma V, Maumus F, Aubriot X, Geering ADW, Teycheney PY. Insertion of badnaviral DNA in the late blight resistance gene (R1a) of brinjal eggplant (Solanum melongena). Front Plant Sci. 2021;12:683681.
Article
PubMed
PubMed Central
Google Scholar
Smit, A.F.A., and Hubley, R. (2008-2010). RepeatModeler Open-1.0. http://www.repeatmasker.org.
Smit, A.F.A., Hubley, R., and Green, P. (1996-2010). RepeatMasker Open-3.0. http://www.repeatmasker.org.
Staginnus C, Gregor W, Mette MF, Teo CH, Borroto-Fernandez EG, Machado ML, et al. Endogenous pararetroviral sequences in tomato (Solanum lycopersicum) and related species. BMC Plant Biol. 2007;7:24.
Article
PubMed
PubMed Central
Google Scholar
Stavolone L, Herzog E, Leclerc D, Hohn T. Tetramerization is a conserved feature of the virion-associated protein in plant pararetroviruses. J Virol. 2001;75:7739–43.
Article
PubMed
PubMed Central
CAS
Google Scholar
Teycheney PY, Geering ADW, Dasgupta I, Hull R, Kreuze JF, Lockhart B, et al. ICTV virus taxonomy profile: Caulimoviridae. J Gen Virol. 2020;101(10):1025.
Article
PubMed
PubMed Central
CAS
Google Scholar
Waterhouse AM, Procter JB, Martin DM, Clamp M, Barton GJ. Jalview version 2--a multiple sequence alignment editor and analysis workbench. Bioinformatics. 2009;25:1189–91.
Article
PubMed
PubMed Central
CAS
Google Scholar
Wilkinson MD, Dumontier M, Aalbersberg IJ, Appleton G, Axton M, Baak A, et al. The FAIR guiding principles for scientific data management and stewardship. Sci Data. 2016;3:160018.
Article
PubMed
PubMed Central
Google Scholar
Xiong Y, Eickbush TH. Origin and evolution of retroelements based upon their reverse transcriptase sequences. EMBO J. 1990;9:3353–62.
Article
PubMed
PubMed Central
CAS
Google Scholar