BMC Genomics 2007, 8:427 http://www.biomedcentral.com/1471-2164/8/427 Whereas the general composition of dispersed repeats rep- resented by various groups of mobile elements resembled that of other plants with complex genomes, our analysis revealed surprising diversity of tandem repeats in the pea genome. In addition to the previously described PisTR-A and PisTR-B repeats [20], thirteen novel families of abun- dant tandem repeats showing genomic organization typi- cal for satellite DNA have been identified. This contrasts with most plants studied so far for which only a single or a few satellites are known [41]. However, whether this is a specific feature of the pea genome or simply a conse- quence of highly efficient tandem repeat identification employing 454 data remains to be seen after more species will be analyzed using this technology. Nevertheless, the availability of such a rich set of satellite repeats differing in monomer length, sequence, and chromosomal locali- zation makes pea an attractive model for studying this type of repeated DNA. For example, our previous investi- gation of PisTR-B repeats using COD-FISH revealed uni- form orientation of its monomers with respect to telomeres on most subtelomeric loci [42]. Extending this study to other satellite families should show if this is a general feature of the satellite arrangement at pea chromo- some termini. Moreover, the wealth of sequence data obtained in this study will allow detailed characterization of sequence variability of individual families and testing if it correlates with the repeat chromosomal localization as was shown for other species [43]. Yet another interesting question concerns the possible lack of a satellite repeat conserved among pea centromeres. Although all pea cen- tromeres seem to contain satellite DNA (Table 2), no fam- ily of the newly identified tandem repeats occupies all centromeres as is common in most plant species charac- terized so far [44,45]. This might either suggest that the genuine centromeric satellite has not been identified in our sequences or that the centromeric sequences in pea underwent less extensive homogenization among non- homologous chromosomes. In addition to the Arabidopsis-type telomeric repeats, two other variants of telomeric minisatellite sequences were identified in the pea genome. Although they were both localized at chromosome termini along with the Arabi- dopsis-type sequences, their origin and role in telomere maintenance are unclear. Occurrence of the mixed minis- atellite telomeric motif was reported from several plants and could be attributed to low fidelity of telomerase [46]. The relatively small number of 454 reads containing telo- meric repeats did not allow us to perform a thorough investigation of their variability; however, there were sev- eral reads including non-perfect or mixed repeat motifs which could support this hypothesis (data not shown). On the other hand, both alternative repeats were also found to form arrays spanning the whole read lengths, which indicates their at least partial arrangement in longer homogeneous arrays. Conclusion This work provided the first detailed survey of repetitive sequences in garden pea. It confirmed the expected high proportion of repeats in the pea genome and revealed that it is mostly attributed to various families of mobile ele- ments. Amplification of a few groups of Ty3/gypsy ele- ments, especially those belonging to Ogre-like retrotransposons, contributed the most to the bulk of pea repeats. Ty1/copia elements were found to be less abun- dant but more diverse in their sequences, occurring in a number of distinct (sub-)families. Other mobile elements including non-LTR retrotransposons (LINEs) and DNA transposons of the MuDR and En/Spm families were also detected. However, their total abundance did not exceed thousands of copies per haploid genome, thus represent- ing only a minor part of pea nuclear DNA. Tandem repeats identified in the pea genome included microsatel- lites, three variants of telomeric minisatellites, and excep- tional diversity of satellite repeats. Localization of newly identified satellite sequences on mitotic chromosomes revealed their family-specific hybridization patterns, pro- viding novel cytogenetic landmarks for chromosome mapping. Although the presented analysis yielded a wealth of infor- mation about the repeat composition of the pea genome, it was also useful in uncovering various limitations of our analytical approaches, which should be improved in the future. In addition to these improvements, a number of novel ways to utilize 454 data in plant genome analysis can be envisioned. They include, for example, repeat masking in genome sequencing projects, detailed investi- gation of intra- and intergenomic repeat variability, and identification of conserved non-coding regulatory sequences. Of special interest is the application of this technology to comparative genomics in a wide range of species, which should provide key information for under- standing evolutionary patterns of repetitive sequences and their impact on genome evolution. Our results demon- strated the feasibility of this approach and revealed that in spite of differences in abundance of individual families, the repeat composition in pea and M. truncatula is similar, whereas both these species share only a few conserved repeats with soybean. Methods Genomic DNA isolation and 454 sequencing Seeds of garden pea (Pisum sativum L. cv. Carrera) were obtained from the Plant Breeding Station at Boršov, Czech Republic. The DNA was extracted from purified nuclei in order to minimize contamination with chloroplast and mitochondrial genomes. The nuclei were isolated from Page 11 of 16 (page number not for citation purposes)