BMC Genomics 2007, 8:427 http://www.biomedcentral.com/1471-2164/8/427 Composition of the most repetitive fraction of the pea genome Using a combination of various tools including sequence similarity searches, conserved protein domain detection, and structure analysis of the contigs, it was possible to assign the most abundant reconstructed sequences into specific classes of repetitive elements (Table 2 and Addi- tional file 3). It was found that the majority of pea repeti- tive DNA is made up of LTR-retrotransposons, with the most prominent group being the Ty3/gypsy-like Ogre ele- ments, which alone were estimated to constitute 20–33% of the genome. Investigation of the sequence variability of contigs representing overlapping fragments of Ogre sequences revealed the presence of several subfamilies of these elements. Further analysis based on quantification of the sequence reads from contig regions that include the primer binding site (PBS) typical for Ogres [26] and com- parison of their surrounding sequences confirmed the occurrence of three distinct subfamilies. It also provided an estimate of their abundance, which was about 30,000 elements for each of the two major subfamilies and 8,000 copies/1C for a minor one. Although other retroelement families were found in con- siderably smaller numbers, there were several elements which made up significant proportions of the genome. They included Peabody, which made up 2–3% of the genome and displayed very low sequence variability sug- gesting its recent amplification. Other important groups of Ty3/gypsy elements were represented by PIGY [24] and Cyclops [27]. Ty1/copia retrotransposons were found to be less frequent, being represented by PDR [28] and a group of SIRE1-like sequences [29]. However, the most abundant was a novel element, Ps-copia-1/751 (Fig. 2C), which made up about 2% of the pea genome. The LTR sequence of this element was estimated to occur in at least 25,000 copies in the pea genome, whereas other regions are less frequent (about 8,000 copies/1C), thus indicating the existence of a large number of solo-LTRs derived from this element (Table 2). Table 2: Repeat composition of the pea genome estimated from genomic abundance of reconstructed contigs Genome representationa Copy numbersb Clusters (contigs) Total GR Genome proportion [%] Copies/1C (domain) Element length [bp] Genome proportion [%] Retroelements Ty3/gypsy Ogre-like Peabody PIGY Cyclops Ty1/copia Ps-copia-1/ 751 full-length solo-LTR SIRE PDR Other copia Other RE DNA transposons MuDR En/Spm Tandem repeats 45S rDNA 5S rDNA PisTR-B Other satellites 77 (632) 5 (42) 23 (70) 15 (52) 6 (14) 9 (87) 6 (24) 16 (26) 17 (111) 7 (24) 5 (9) 1 (6) 1 (3) 1 (7) 16 (73) 6,754,965 703,484 361,389 221,925 690,339 548,280 214,755 101,805 878,773 68,247 50,845 348,987 13,134 147,113 381,148 Total : 20.30 2.11 1.09 0.67 2.07 1.65 0.65 0.31 2.64 0.21 0.15 1.05 0.04 0.44 1.15 34.5 % 65,000 (RT, PBS) 16,000 (RT) 4,700 (RT) 2,700 (RT) 8,000 (RT) 9,000 1,100 (RT) 22,000 8,000 13,600 12,300 8,000 1,400 4,000 5,300 8,680 33.26 2.98 1.49 0.77 1.49 0.29 (1.65) 0.10 (0.31) (2.64) (0.21) (0.15) 1.07 (0.04) (0.44) (1.15) 48.0 % aGenome proportion of individual groups of repeats was estimated from the sum of genome representation (GR) values of corresponding clusters of contigs. b Estimates based on genomic copy numbers inferred from the read depth of contigs including conserved sequence domains (RT, reverse transcriptase; PBS, primer binding site). Genome proportion of the repeats was calculated using the length of the complete elements and therefore it is provided only for repeat families with known full-length copies in the pea genome. Page 6 of 16 (page number not for citation purposes)