The classification and nomenclature of endogenous viruses of the family Caulimoviridae

Baillie GJ, van de Lagemaat LN, Baust C, Mager DL (2004) Multiple groups of endogenous betaretroviruses in mice, rats, and other mammals. J Virol 78:5784–5798 Belshaw R, Pereira V, Katzourakis A, Talbot G, Pačes J, Burt A, Tristem M (2004) Long-term reinfection of the human genome by endogenous retroviruses. Proc Natl Acad Sci USA 101:4894–4899 Belshaw R, Dawson ALA, Woolven-Allen J, Redding J, Burt A, Tristem M (2005) Genomewide screening reveals high levels of insertional polymorphism in the human endogenous retrovirus family HERV-K(HML2): implications for present-day activity. J Virol 79:12507–12514 Boller K, Schonfeld K, Lischer S, Fischer N, Hoffmann A, Kurth R, Tonjes RR (2008) Human endogenous retrovirus HERV-K113 is capable of producing intact viral particles. J Gen Virol 89:567–572 Bousalem M, Douzery E, Seal S (2008) Taxonomy, molecular phylogeny and evolution of plant reverse transcribing viruses (family Caulimoviridae) inferred from full-length genome and reverse transcriptase sequences. Arch Virol 153:1085–1102 Bremer K (1994) Branch support and tree stability. Cladistics-Int J Willi Hennig Soc 10:295–304 Calvert LA, Ospina MD, Shepherd RJ (1995) Characterization of cassava vein mosaic virus: a distinct plant pararetrovirus. J Gen Virol 76:1271–1278 Davies JF 2nd, Hostomska Z, Hostomsky Z, Jordan SR, Matthews DA (1991) Crystal structure of the ribonuclease H domain of HIV-1 reverse transcriptase. Science 252:88–95 de Kochko A, Verdaguer B, Taylor N, Carcamo R, Beachy RN, Fauquet C (1998) Cassava vein mosaic virus (CsVMV), type species for a new genus of plant double stranded DNA viruses? Arch Virol 143:945–962 Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA (2005) Virus taxonomy: classification and nomenclature of viruses. Eighth report of the international committee on taxonomy of viruses. Elsevier Academic Press, San Diego Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791 Flockerzi A, Ruggieri A, Frank O, Sauter M, Maldener E, Kopper B, Wullich B, Seifarth W, Muller-Lantzsch N, Leib-Mosch C, Meese E, Mayer J (2008) Expression patterns of transcribed human endogenous retrovirus HERV-K(HML-2) loci in human tissues and the need for a HERV Transcriptome project. BMC Genomics 9:354 Gambley CF, Geering ADW, Steele V, Thomas JE (2008) Identification of viral and non-viral reverse transcribing elements in pineapple (Ananas comosus), including members of two new badnavirus species. Arch Virol 153:1599–1604 Gayral P, Noa-Carrazana J-C, Lescot M, Lheureux F, Lockhart BEL, Matsumoto T, Piffanelli P, Iskra-Caruana M-L (2008) A single Banana streak virus integration event in the banana genome as the origin of infectious endogenous pararetrovirus. J Virol 82:6697–6710 Geering ADW, Olszewski NE, Harper G, Lockhart BEL, Hull R, Thomas JE (2005) Banana contains a diverse array of endogenous badnaviruses. J Gen Virol 86:511–520 Huelsenbeck JP, Ronquist F (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17:754–755 Hull R, Covey SN (1995) Retroelements: Propagation and adaptation. Virus Genes 11:105–118 Hull R (2001) Classifying reverse transcribing elements: a proposal and challenge to the ICTV. Arch Virol 146:2255–2261 Jakowitsch J, Mette MF, van der Winden J, Matzke MA, Matzke AJM (1999) Integrated pararetroviral sequences define a unique class of dispersed repetitive DNA in plants. Proc Natl Acad Sci USA 96:13241–13246 Johnson MS, McClure MA, Feng DF, Gray J, Doolittle RF (1986) Computer analysis of retroviral pol genes: assignment of enzymatic functions to specific sequences and homologies with nonviral enzymes. Proc Natl Acad Sci USA 83:7648–7652 Katzourakis A, Tristem M, Pybus OG, Gifford RJ (2007) Discovery and analysis of the first endogenous lentivirus. Proc Natl Acad Sci 104:6261–6265 Kunii M, Kanda M, Nagano H, Uyeda I, Kishima Y, Sano Y (2004) Reconstruction of putative DNA virus from endogenous rice tungro bacilliform virus-like sequences in the rice genome: implications for integration and evolution. BMC Genomics 5:14 Lescot M, Piffanelli P, Ciampi A, Ruiz M, Blanc G, Leebens-Mack J, da Silva F, Santos C, D’Hont A, Garsmeur O, Vilarinhos A, Kanamori H, Matsumoto T, Ronning C, Cheung F, Haas B, Althoff R, Arbogast T, Hine E, Pappas G, Sasaki T, Souza M, Miller R, Glaszmann J-C, Town C (2008) Insights into the Musa genome: syntenic relationships to rice and between Musa species. BMC Genomics 9:58 Lim D, Gregorio GG, Bingman C, Martinez-Hackert E, Hendrickson WA, Goff SP (2006) Crystal structure of the Moloney murine leukemia virus RNase H domain. J Virol 80:8379–8389 Lockhart BE, Menke J, Dahal G, Olszewski NE (2000) Characterization and genomic analysis of tobacco vein clearing virus, a plant pararetrovirus that is transmitted vertically and related to sequences integrated in the host genome. J Gen Virol 81:1579–1585 Melcher U (2000) The ‘30 K’ superfamily of viral movement proteins. J Gen Virol 81:257–266 Ndowora T, Dahal G, LaFleur D, Harper G, Hull R, Olszewski N, Lockhart B (1999) Evidence that badnavirus infection in Musa can originate from integrated sequences. Virology 255:214–220 Pahalawatta V, Druffel K, Pappu H (2008) A new and distinct species in the genus Caulimovirus exists as an endogenous plant pararetroviral sequence in its host, Dahlia variabilis. Virology 376:253–257 Poch O, Sauvaget I, Delarue M, Tordo N (1989) Identification of four conserved motifs among the RNA-dependent polymerase encoding elements. The EMBO Journal 8:3867–3874 Pooggin MM, Fütterer J, Skryabin KG, Hohn T (1999) A short open reading frame terminating in front of a stable hairpin is the conserved feature in pregenomic RNA leaders of plant pararetroviruses. J Gen Virol 80:2217–2228 Posada D, Crandall KA (1998) MODELTEST: testing the model of DNA substitution. Bioinformatics 14:817–818 Rice P, Longden I, Bleasby A (2000) EMBOSS: The European molecular biology open software suite. Trends Genet 16:276–277 Richert-Pöggeler KR, Noreen F, Schwarzacher T, Harper G, Hohn T (2003) Induction of infectious petunia vein clearing (pararetro) virus from endogenous provirus in petunia. EMBO J 22:4836–4845 Schultz SJ, Champoux JJ (2008) RNase H activity: structure, specificity, and function in reverse transcription. Virus Res 134:86–103 Staginnus C, Richert-Poggeler KR (2006) Endogenous pararetroviruses: two-faced travelers in the plant genome. Trends Plant Sci 11:485–491 Staginnus C, Gregor W, Mette MF, Teo C, Borroto-Fernandez E, Machado ML, Matzke M, Schwarzacher T (2007) Endogenous pararetroviral sequences in tomato (Solanum lycopersicum) and related species. BMC Plant Biol 7:24 Staginnus C, Iskra-Caruana M, Lockhart B, Hohn T, Richert-Pöggeler K (2009) Suggestions for a nomenclature of endogenous pararetroviral sequences in plants. Arch Virol 154:1189–1193 Stavolone L, Herzog E, Leclerc D, Hohn T (2001) Tetramerization is a conserved feature of the virion-associated protein in plant pararetroviruses. J Virol 75:7739–7743 Stoye JP (2001) Endogenous retroviruses: Still active after all these years? Curr Biol 11:R914–R916 Swofford DL (2002) PAUP*. Phylogenetic analysis using parsimony (*and other methods). Sinauer Associates, Sunderland, MA Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599 Temin HM (1985) Reverse transcription in the eukaryotic genome: retroviruses, pararetroviruses, retrotransposons, and retrotranscripts. Mol Biol Evol 2:455–468 Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 24:4876–4882 Torruella M, Gordon K, Hohn T (1989) Cauliflower mosaic virus produces an aspartic proteinase to cleave its polyproteins. EMBO J 8:2819–2825 Xiong Y, Eikbush TH (1990) Origin and evolution of retroelements based upon their reverse transcriptase sequences. EMBO J 9:3353–3362