BMC Genomics 2007, 8:427 http://www.biomedcentral.com/1471-2164/8/427 12. Manetti ME, Rossi M, Costa APP, Clausen AM, Van Sluys MA: Radia- tion of the Tnt1 retrotransposon superfamily in three Solanaceae genera. BMC Evol Biol 2007, 7:. 13. Nouzova M, Neumann P, Navratilova A, Galbraith DW, Macas J: Microarray-based survey of repetitive genomic sequences in Vicia spp. Plant Mol Biol 2001, 45:229-244. 14. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen ZT, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer MLI, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu PG, Begley RF, Rothberg JM: Genome sequencing in microfabricated high-density picoli- tre reactors. Nature 2005, 437:376-380. 15. Smith MG, Gianoulis TA, Pukatzki S, Mekalanos JJ, Ornston LN, Ger- stein M, Snyder M: New insights into Acinetobacter baumannii pathogenesis revealed by high-density pyrosequencing and transposon mutagenesis. Genes Dev 2007, 21:601-614. 16. Noonan JP, Coop G, Kudaravalli S, Smith D, Krause J, Alessi J, Chen F, Platt D, Paabo S, Pritchard JK, Rubin EM: Sequencing and analy- sis of Neanderthal genomic DNA. Science 2006, 314:1113-1118. 17. Cheung F, Haas BJ, Goldberg SM, May GD, Xiao Y, Town CD: Sequencing Medicago truncatula expressed sequenced tags using 454 Life Sciences technology. BMC Genomics 2006, 7:272. 18. Plant DNA C-values database [http://www.kew.org/cval/] 19. Swaminathan K, Varala K, Hudson ME: Global repeat discovery and estimation of genomic copy number in a large, complex genome using a high-throughput 454 sequence survey. BMC Genomics 2007, 8:. 20. Neumann P, Nouzova M, Macas J: Molecular and cytogenetic analysis of repetitive DNA in pea (Pisum sativum L.). Genome 2001, 44:716-728. 21. Neumann P, Pozarkova D, Macas J: Highly abundant pea LTR ret- rotransposon Ogre is constitutively transcribed and partially spliced. Plant Mol Biol 2003, 53:399-410. 22. Macas J, Neumann P, Pozarkova D: Zaba: a novel miniature trans- posable element present in genomes of legume plants. Mol Genet Genomics 2003, 269:624-631. 23. Macas J, Koblizkova A, Neumann P: Characterization of Stowa- way MITEs in pea (Pisum sativum L.) and identification of their potential master elements. Genome 2005, 48:831-839. 24. Neumann P, Pozarkova D, Koblizkova A, Macas J: PIGY, a new plant envelope-class LTR retrotransposon. Mol Genet Genomics 2005, 273:43-53. 25. Pertea G, Huang XQ, Liang F, Antonescu V, Sultana R, Karamycheva S, Lee Y, White J, Cheung F, Parvizi B, Tsai J, Quackenbush J: TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics 2003, 19:651-652. 26. Macas J, Neumann P: Ogre elements – A distinct group of plant Ty3/gypsy-like retrotransposons. Gene 2007, 390:108-116. 27. Chavanne F, Zhang DX, Liaud MF, Cerff R: Structure and evolu- tion of Cyclops: a novel giant retrotransposon of the Ty3/ Gypsy family highly amplified in pea and other legume spe- cies. Plant Mol Biol 1998, 37:363-375. 28. Lee D, Ellis THN, Turner L, Hellens RP, Cleary WG: A copia-like element in Pisum demonstrates the uses of dispersed repeated sequences in genetic-analysis. Plant Mol Biol 1990, 15:707-722. 29. Laten HM, Havecker ER, Farmer LM, Voytas DF: SIRE1, an endog- enous retrovirus family from Glycine max, is highly homog- enous and evolutionarily young. Mol Biol Evol 2003, 20:1222-1230. 30. Xiong Y, Eickbush TH: Origin and evolution of retroelements based upon their reverse-transcriptase sequences. EMBO J 1990, 9:3353-3362. 31. Richards EJ, Ausubel FM: Isolation of a higher eukaryotic tel- omere from Arabidopsis thaliana. Cell 1988, 53:127-136. 32. Li RQ, Ye J, Li SG, Wang J, Han YJ, Ye C, Wang J, Yang HM, Yu J, Wong GKS, Wang J: ReAS: Recovery of ancestral sequences for transposable elements from the unassembled reads of a whole genome shotgun. PLoS Comput Biol 2005, 1:313-321. 33. Elsik CG, Williams CG: Retroelements contribute to the excess low-copy-number DNA in pine. Mol Gen Genet 2000, 264:47-55. 34. Rabinowicz PD, Bennetzen JL: The maize genome as a model for efficient sequence analysis of large plant genomes. Curr Opin Plant Biol 2006, 9:149-156. 35. Feschotte C, Jiang N, Wessler SR: Plant transposable elements: Where genetics meets genomics. Nat Rev Genet 2002, 3:329-341. 36. Bennetzen JL, Ma JX, Devos K: Mechanisms of recent genome size variation in flowering plants. Ann Bot 2005, 95:127-132. 37. Gao LH, McCarthy EM, Ganko EW, McDonald JF: Evolutionary his- tory of Oryza sativa LTR retrotransposons: a preliminary sur- vey of the rice genome sequences. BMC Genomics 2004, 5:. 38. Hill P, Burford D, Martin DMA, Flavell AJ: Retrotransposon popu- lations of Vicia species with varying genome size. Mol Genet Genomics 2005, 273:371-381. 39. Flavell , Smith , Kumar : Extreme heterogeneity of Ty1-copia group retrotransposons in plants. Mol Gen Genet 1992, 231:233-242. 40. 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 Res 2007, 17:1072-1081. 41. Macas J, Meszaros T, Nouzova M: PlantSat: a specialized data- base for plant satellite repeats. Bioinformatics 2002, 18:28-35. 42. Navratilova A, Neumann P, Macas J: Long-range organization of plant satellite repeats investigated using strand-specific FISH. Cytogenet Genome Res 2005, 109:58-62. 43. Macas J, Navratilova A, Koblizkova A: Sequence homogenization and chromosomal localization of VicTR-B satellites differ between closely related Vicia species. Chromosoma 2006, 115:437-447. 44. Kulikova O, Geurts R, Lamine M, Kim DJ, Cook DR, Leunissen J, de Jong H, Roe BA, Bisseling T: Satellite repeats in the functional centromere and pericentromeric heterochromatin of Medi- cago truncatula. Chromosoma 2004, 113:276-283. 45. Jiang JM, Birchler JA, Parrott WA, Dawe RK: A molecular view of plant centromeres. Trends Plant Sci 2003, 8:570-575. 46. Fajkus J, Sykorova E, Leitch AR: Telomeres in evolution and evo- lution of telomeres. Chromosome Res 2005, 13:469-479. 47. Vershinin AV, Heslop-Harrison JS: Comparative analysis of the nucleosomal structure of rye, wheat and their relatives. Plant Mol Biol 1998, 36:149-161. 48. The NCBI Trace Archive [http://www.ncbi.nlm.nih.gov/Traces/] 49. Altschul SF, Madden TL, Schaffer AA, Zhang JH, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402. 50. [http://www.bioperl.org/]. 51. [http://w3lamc.umbr.cas.cz/pisum_454/]. 52. Marchler-Bauer A, Anderson JB, DeWeese-Scott C, Fedorova ND, Geer LY, He SQ, Hurwitz DI, Jackson JD, Jacobs AR, Lanczycki CJ, Liebert CA, Liu CL, Madej T, Marchler GH, Mazumder R, Nikolskaya AN, Panchenko AR, Rao BS, Shoemaker BA, Simonyan V, Song JS, Thiessen PA, Vasudevan S, Wang YL, Yamashita RA, Yin JJ, Bryant SH: CDD: a curated Entrez database of conserved domain align- ments. Nucleic Acids Res 2003, 31:383-387. 53. Sonnhammer ELL, Durbin R: A dot-matrix program with dynamic threshold control suited for genomic DNA and pro- tein sequence analysis. Gene 1995, 167:GC1-GC10. 54. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG: The CLUSTAL_X windows interface: flexible strategies for mul- tiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997, 25:4876-4882. 55. Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichie- wicz J: Repbase update, a database of eukaryotic repetitive elements. Cytogenet Genome Res 2005, 110:462-467. 56. Jurka J: Repbase Update – a database and an electronic jour- nal of repetitive elements. Trends Genet 2000, 16:418-420. 57. Zmasek CM, Eddy SR: ATV: display and manipulation of anno- tated phylogenetic trees. Bioinformatics 2001, 17:383-384. 58. Rambaut A, Charleston M: TreeEdit – Phylogeny Editor and Manipulator. [http://evolve.zoo.ox.ac.uk/software/TreeEdit/ main.html]. Page 15 of 16 (page number not for citation purposes)