Large tandem repeats of grass frog (Rana temporaria) in silico and in situ.

BACKGROUND: Genomes of higher eukaryotes contain a large fraction of non-coding repetitive DNA, including tandem repeats (TRs) and transposable elements (TEs). The impact of TRs on genome structure and function and the importance of TR transcripts have been described for several model species. Amphibians have one of the most diverse genome sizes among vertebrates, attributed to the abundance of repetitive non-coding DNA. Consequently, amphibians are good models for the analysis of repetitive sequences, including TRs. However, few studies have focused on amphibian genomes. RESULTS: Bioinformatic analyses were performed to characterise the content and localisation of TRs in the sequenced grass frog Rana temporaria genome. By applying different bioinformatic approaches, 76 TR families and 314 single TR arrays (not grouped into families) were identified. Each TR was characterised on the basis of chromosomal position, monomer length and variability and GC content. Bioinformatic analysis revealed a great diversity of TRs, with a clear predominance of TRs with short monomers (< 100 bp), although TRs with long monomers (> 1000 bp) also exist. The six most abundant TRs were successfully mapped by fluorescence in situ hybridization (FISH), which highlighted the presence of specific TR sequences in strategic chromosomal regions, i.e., the pericentromeric regions. A comparison of the results of in situ and in silico TR mapping revealed some inaccuracies in the assembly of heterochromatic regions. A putative new non-autonomous TE called "FEDoR" (Frog Element Dispersed organised Repeat) is also described. FEDoR is ∼ 3.5 kb in length, has no significant similarity to any known TE family, contains multiple internal TR motifs, and is flanked on both sides by pairs of inverted repeat sequences (IRSs) and target site duplications (TSDs). CONCLUSION: Characterisation of TRs in this frog species has provided some insights regarding TR biology in Anuran amphibians.