BMC Genomics 2007, 8:427 http://www.biomedcentral.com/1471-2164/8/427 Authors' contributions JM conceived the study and carried out most of the bioin- formatics analysis. PN participated in repeat identification and conducted phylogenetic analysis of retroelements. AN carried out FISH experiments. All authors contributed to the manuscript preparation and approved its final ver- sion. Additional material Additional file 1 Repetitive sequences and their copy number estimates used for the evaluation of repeat representation in 454 data. The table provides GenBank accession numbers, descriptions and experimentally determined copy numbers of selected pea repeats together with calculations of their genomic abundance based on the 454 data. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-8-427-S1.pdf] Additional file 2 Sorted list of 50 reconstructed contigs with the highest genome represen- tation. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-8-427-S2.xls] Additional file 3 Assignment of clusters of reconstructed contigs to individual repeat fami- lies. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-8-427-S3.xls] Additional file 4 Phylogenetic analysis of Ty3/gypsy elements based on their reverse transcriptase domains. Phylogenetic trees show relationship of reverse transcriptase domains identified in pea 454 contigs to those from selected plant retroelements. Only contigs bearing complete or marginally trun- cated (marked with asterisks) RT domains were used for analysis and their names and positions are labeled with yellow boxes. Contigs contain- ing only partial RT sequences were assigned to the trees based on their sequence similarity to full-length domains (labeled as "best hit"). Copy numbers of elements belonging to individual clades are provided in Figure 4. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-8-427-S4.pdf] Additional file 5 Phylogenetic analysis of Ty1/copia elements based on their reverse transcriptase domains. Phylogenetic trees show relationship of reverse transcriptase domains identified in pea 454 contigs to those from selected plant retroelements. Only contigs bearing complete or marginally trun- cated (marked with asterisks) RT domains were used for analysis and their names and positions are labeled with yellow boxes. Contigs contain- ing only partial RT sequences were assigned to the trees based on their sequence similarity to full-length domains (labeled as "best hit"). Copy numbers of elements belonging to individual clades are provided in Figure 4. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-8-427-S5.pdf] Additional file 6 PCR primers used for preparation of FISH probes for reconstructed tan- dem repeats. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-8-427-S6.pdf] Acknowledgements This work was supported by grants IAA500960702 and AVOZ50510513 from the Academy of Sciences of the Czech Republic, and LC06004 from the Ministry of Education, Youth and Sports of the Czech Republic. We thank J. Látalová and H. ŠtЕpančíková for excellent technical assistance, and S. M. Rafelski for assistance with preparation of the manuscript. References 1. Shapiro JA, von Sternberg R: Why repetitive DNA is essential to genome function. Biol Rev 2005, 80:227-250. 2. Bennetzen JL: Patterns in grass genome evolution. Curr Opin Plant Biol 2007, 10:176-181. 3. Morgante M, De Paoli E, Radovic S: Transposable elements and the plant pan-genomes. Curr Opin Plant Biol 2007, 10:149-155. 4. Slotkin RK, Martienssen R: Transposable elements and the epi- genetic regulation of the genome. Nat Rev Genet 2007, 8:272-285. 5. 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