Bousios et al. BMC Genomics 2010, 11:89 http://www.biomedcentral.com/1471-2164/11/89 Abbreviations PPT: polypurine tract; LTR: long terminal repeat; ENV: envelope; VLP: virus-like particle; AP: aspartic protease; INT: integrase; RT: reverse transcriptase; RH: RNaseH; DBF: DNA binding factor; RM: repeated motif; UTR: untranslated region; PBS: primer binding site; ICTV: International Committee on the Taxonomy of Viruses; ORF: open reading frame; IR: inverted repeat. Acknowledgements We thank T. Thedosiou, T. Schwarzacher, E. Simeonidis and V. Apostolidou for reading and improving this manuscript. AB and ND were supported by the BioSapiens Network of Excellence (contract number LSHG-CT-2003- 503265). Author details 1Department of Biology and Environmental Science, School of Life Sciences, University of Sussex, Brighton, UK. 2Institute of Agrobiotechnology, Centre for Research and Technology Hellas, Thessaloniki 57001, Greece. 3Department of Genetics and Plant Breeding, Aristotle University of Thessaloniki AUTH, Thessaloniki 54006, Greece. Authors’ contributions AB conceived and designed the study, carried out the data collection, analysis, and interpretation, and drafted the manuscript. ND carried out pattern discovery with the TEIRESIAS algorithm, assisted in data interpretation and critically revised the manuscript. AT assisted in data interpretation and critically revised the manuscript. SP conceived and designed the study, and critically revised the manuscript. All authors read and approved the final manuscript. Received: 11 November 2009 Accepted: 4 February 2010 Published: 4 February 2010 References 1. Hansen C, Heslop-Harrison JS: Sequences and phylogenies of plant pararetroviruses, viruses, and transposable elements. Advances in Botanical Research Incorporating Advances in Plant Pathology 2004, 41:165-193. 2. Kumar A, Bennetzen JL: Plant retrotransposons. Annu Rev Genet 1999, 33:479-532. 3. Bousios A, Saldana-Oyarzabal I, Valenzuela-Zapata AG, Wood C, Pearce SR: Isolation and characterization of Ty1-copia retrotransposon sequences in the blue agave (Agave tequilana Weber var. azul) and their development as SSAP markers for phylogenetic analysis. Plant Science 2007, 172(2):291-298. 4. Feschotte C, Jiang N, Wessler SR: Plant transposable elements: Where genetics meets genomics. Nature Reviews Genetics 2002, 3(5):329-341. 5. Pearce SR, Harrison G, HeslopHarrison PJS, Flavell AJ, Kumar A: Characterization and genomic organization of Ty1-copia group retrotransposons in rye (Secale cereale). Genome 1997, 40(5):617-625. 6. Vitte C, Panaud O: LTR retrotransposons and flowering plant genome size: emergence of the increase/decrease model. Cytogenetic and Genome Research 2005, 110(1-4):91-107. 7. Pereira V: Insertion bias and purifying selection of retrotransposons in the Arabidopsis thaliana genome. Genome Biol 2004, 5(10):R79. 8. McCarthy EM, Liu J, Lizhi G, McDonald JF: Long terminal repeat retrotransposons of Oryza sativa. Genome Biol 2002, 3(10):RESEARCH0053. 9. Baucom RS, Estill JC, Chaparro C, Upshaw N, Jogi A, Deragon JM, Westerman RP, SanMiguel PJ, Bennetzen JL: Exceptional Diversity, Non- Random Distribution, and Rapid Evolution of Retroelements in the B73 Maize Genome. Plos Genetics 2009, 5(11):e1000732. 10. Schnable PS, Ware D, Fulton RS, Stein JC, Wei FS, Pasternak S, Liang CZ, Zhang JW, Fulton L, Graves TA, Minx P, Reily AD, Courtney L, Kruchowski SS, Tomlinson C, Strong C, Delehaunty K, Fronick C, Courtney B, Rock SM, Belter E, Du FY, Kim K, Abbott RM, Cotton M, Levy A, Marchetto P, Ochoa K, Jackson SM, Gillam B, et al: The B73 Maize Genome: Complexity, Diversity, and Dynamics. Science 2009, 326(5956):1112-1115. 11. Vicient CM, Suoniemi A, Anamthamat-Jonsson K, Tanskanen J, Beharav A, Nevo E, Schulman AH: Retrotransposon BARE-1 and its role in genome evolution in the genus Hordeum. Plant Cell 1999, 11(9):1769-1784. 12. Wicker T, Sabot F, Hua-Van A, Bennetzen JL, Capy P, Chalhoub B, Flavell A, Leroy P, Morgante M, Panaud O, Paux E, SanMiguel P, Schulman AH: A Page 13 of 14 unified classification system for eukaryotic transposable elements. Nature Reviews Genetics 2007, 8(12):973-982. 13. Peterson-Burch BD, Voytas DF: Genes of the Pseudoviridae (Ty1/copia retrotransposons). Mol Biol Evol 2002, 19(11):1832-1845. 14. Grandbastien MA, Lucas H, Morel JB, Mhiri C, Vernhettes S, Casacuberta JM: The expression of the tobacco Tnt1 retrotransposon is linked to plant defense responses. Genetica 1997, 100(1-3):241-252. 15. Vernhettes S, Grandbastien MA, Casacuberta JM: In vivo characterization of transcriptional regulatory sequences involved in the defence-associated expression of the tobacco retrotransposon Tnt1. Plant Molecular Biology 1997, 35(5):673-679. 16. Wilhelm M, Wilhelm FX: Reverse transcription of retroviruses and LTR retrotransposons. Cellular and Molecular Life Sciences 2001, 58(9):1246-1262. 17. Boeke JD, Eickbush TH, Sandmeyer SB, Voytas DF: Index of Viruses - Pseudoviridae (2006). ICTVdB - The Universal Virus Database, version 4 Columbia University, New York, USABuchen-Osmond C 2006. 18. Havecker ER, Gao X, Voytas DF: The sireviruses, a plant-specific lineage of the Ty1/copia retrotransposons, interact with a family of proteins related to dynein light chain. Plant Physiol 2005, 139(2):857-868. 19. Havecker ER, Gao X, Voytas DF: The diversity of LTR retrotransposons. Genome Biol 2004, 5(6):225. 20. Gao X, Havecker ER, Baranov PV, Atkins JF, Voytas DF: Translational recoding signals between gag and pol in diverse LTR retrotransposons. RNA-Publ RNA Soc 2003, 9(12):1422-1430. 21. Nagaki K, Song JQ, Stupar RM, Parokonny AS, Yuan QP, Ouyang S, Liu J, Hsiao J, Jones KM, Dawe RK, Buell CR, Jiang JM: Molecular and cytological analyses of large tracks of centromeric DNA reveal the structure and evolutionary dynamics of maize centromeres. Genetics 2003, 163(2):759-770. 22. Holligan D, Zhang XY, Jiang N, Pritham EJ, Wessler SR: The transposable element landscape of the model legume Lotus japonicus. Genetics 2006, 174(4):2215-2228. 23. Kenward KD, Bai D, Ban MR, Brandle JE: Isolation and characterization of Tnd-1, a retrotransposon marker linked to black root rot resistance in tobacco. Theor Appl Genet 1999, 98(3-4):387-395. 24. Xiong Y, Eickbush TH: Origin and Evolution of Retroelements Based Upon Their Reverse-Transcriptase Sequences. Embo J 1990, 9(10):3353-3362. 25. Rigoutsos I, Floratos A: Combinatorial pattern discovery in biological sequences: the TEIRESIAS algorithm. Bioinformatics 1998, 14(1):55-67. 26. Goff SP: Genetics of Retroviral Integration. Annu Rev Genet 1992, 26:527-544. 27. Higo K, Ugawa Y, Iwamoto M, Korenaga T: Plant cis-acting regulatory DNA elements (PLACE) database: 1999. Nucleic Acids Res 1999, 27(1):297-300. 28. Gardiner-Garden M, Frommer M: Cpg Islands in Vertebrate Genomes. Journal of Molecular Biology 1987, 196(2):261-282. 29. Ashikawa I: Gene-associated CpG islands in plants as revealed by analyses of genomic sequences. Plant J 2001, 26(6):617-625. 30. Ashikawa I, Numa H, Sakata K: Segmental distribution of genes harboring a CpG island-like region on rice chromosomes. Molecular Genetics and Genomics 2006, 275(1):18-25. 31. Grace ML, Chandrasekharan MB, Hall TC, Crowe AJ: Sequence and spacing of TATA box elements are critical for accurate initiation from the beta- phaseolin promoter. J Biol Chem 2004, 279(9):8102-8110. 32. Wang H, Liu JS: LTR retrotransposon landscape in Medicago truncatula: more rapid removal than in rice. BMC Genomics 2008, 9. 33. Bugreev DV, Baranova S, Zakharova OD, Parissi V, Desjobert C, Sottofattori E, Balbi A, Litvak S, Tarrago-Litvak L, Nevinsky GA: Dynamic, thermodynamic, and kinetic basis for recognition and transformation of DNA by human immunodeficiency virus type 1 integrase. Biochemistry 2003, 42(30):9235-9247. 34. Wicker T, Keller B: Genome-wide comparative analysis of copia retrotransposons in Triticeae, rice, and Arabidopsis reveals conserved ancient evolutionary lineages and distinct dynamics of individual copia families. Genome Research 2007, 17:1072-1081. 35. Wright DA, Voytas DF: Athila4 of Arabidopsis and Calypso of soybean define a lineage of endogenous plant retroviruses. Genome Research 2002, 12(1):122-131. 36. Bowman EH, Pathak VK, Hu WS: Efficient initiation and strand transfer of polypurine tract-primed plus-strand DNA prevent strand transfer of internally initiated plus-strand DNAs. Journal of Virology 1996, 70(3):1687-1694.