BMC Genomics 2007, 8:427 http://www.biomedcentral.com/1471-2164/8/427 Overall diversity of retrotransposons was also studied by their classification based on the RT domains, which are conserved enough to be reliably identified based on pro- tein similarity searches with RT domains from already known retrotransposons. The searches resulted in finding 452 contigs with similarity to RT domains (E-value <= 0.001). Of them, 222 contigs were related to Ty1/copia, 217 to Ty3/gypsy, and only 13 to LINE retrotransposons. Only four Ty1/copia-like and seven Ty3/gypsy-like contigs spanned full-length RT domains as defined by [30] while the rest contained partial sequences due to the short length and/or termination within the RT domain. Phylo- genetic analysis of RT sequences belonging to Ty1/copia and Ty3/gypsy groups revealed that most Ty3/gypsy-like RT domains are related to the previously described pea ret- rotransposon families Ogre, Peabody, PIGY and Cyclops (Additional file 4). On the other hand, Ty1/copia-like RT domains were related to a greater number of retrotranspo- son families, most of which have not been previously identified in the pea genome (Additional file 5). RT domains were also used to estimate the copy number of retrotransposons present in pea. These elements were esti- mated to occur in about 141,000 copies/1C, of which 46,000 (32.6 %) belong to Ty1/copia, 94,000 (67%) to Ty3/gypsy and ~500 (0,4%) to the LINE group (Fig. 4). The highest copy number was estimated for Ogre retro- transposons, which amplified themselves to about 64,000 copies. More detailed analysis of Ogre-like RT domains confirmed the occurrence of distinct Ogre subfamilies sharing their best similarities with elements from different branches of the Ogre clade (Additional file 4). The most abundant were subfamilies from PS and VP/VM branches having about 24,000 and 32,000 copies, respectively (Additional file 4 and Fig. 4). Thus, the total copy number of Ogre elements as well as the abundance of the two major subfamilies were in agreement with estimates based on the abundance of PBS sites described above. Two other clades of Ty3/gypsy retrotransposons, Peabody and enve- lope-like retrotransposons (including PIGY and Cyclops), were estimated to have 16,000 and 12,000 copies, respec- tively. Although Ty1/copia retrotransposons were less fre- quent than Ty3/gypsy, elements from clades 3 and 5 (Additional file 5) reached high copy numbers (10,000 and 26,000 copies, respectively; Fig. 4). Interestingly, clade 3 contained elements from Graminae species such as barley (BARE-1), rice (RIRE-1), and oats (OARE-1) clus- tered together with a newly identified pea element Ps- copia-1/751. Clade 5 contains elements similar to SIRE1, an envelope-like retrotransposon from soybean [29]. It is not clear yet, however, whether all elements within this clade are genuine envelope-like retrotransposons, i.e. whether they all bear envelope-like gene. Compared to the sum of retroelement sequences, other classes of repeats represented significantly smaller parts of CbFailgasesusdrifeoicna4ttioheniranrdevceorpsey tnruamnsbcerripstoasfepedaomreatirnostransposons Classification and copy numbers of pea retrotrans- posons based on their reverse transcriptase domains. Individual groups of retrotransposons were classified accord- ing to their position within the phylogenetic trees or based on their best BLAST hits (Additional files 4 and 5). Ogre retro- transposons were further classified into several subfamilies as shown in the Additional file 4. the pea genome (Table 2). Identified DNA transposons did not exceed 0.5%, and tandem repeats including rDNA gene clusters and various satellite sequences represented about 2.5% of the pea genome. We have also investigated the abundance of micro- and minisatellite repeats with monomers from 2 to 10 bp. Since these repeats usually occur in the genome as short stretches of repeated mono- mers dispersed within unrelated sequences, we analyzed their frequency in unassembled sequence reads instead of contigs. When considering arrays of at least five consecu- tive monomers, microsatellites (AAT)n, (AT)n, and (AG)n were found to be most frequent, occurring in about 80,000 genomic loci. Other microsatellite motifs were less abundant and there were differences over two orders of magnitude in the frequency of various microsatellites within the reads (data not shown). Special attention was paid to detection of telomeric repeats. The Arabidopsis-type telomeric sequence (TTTAGGG)n [31] was present in 14 reads, with an average number of 18 repetitions per read. This gives a rough esti- mate of about 229 kb of this sequence in the pea genome, and agrees with experimental observations of this repeat at termini of all chromosomes (data not shown). How- ever, two additional telomere-like repeats were found in the analyzed reads – (TTAGG)n and (TTTAGG)n. Although both were less frequent than the Arabidopsis-type repeat, Page 7 of 16 (page number not for citation purposes)