Genet et al. BMC Genomics 2011, 12:314 http://www.biomedcentral.com/1471-2164/12/314 Preliminary survey of repeat content from rainbow trout genome Few studies have reported the identification and charac- terization of repeat elements in salmonids, resulting in the absence of sufficient repeat masking data set for rainbow trout. Repbase update release 13.05 contains only 145 ancestral shared repeats and one lineage-speci- fic repeat for rainbow trout, and for salmon, 141 ances- tral shared repeats and five lineage-specific repeats [36]. Consequently, masking of rainbow trout BES using RepBase 13.05 generated only 1.66% of masked sequences. Therefore, we used the BES data to generate a new rainbow trout repeat library. This database con- tains 735 putative elements and was named INRA RT rep1.0 (available as Additional file 1). Repeat element analysis using the new INRA RT rep1.0 library masked almost 59.5% of the BES database in base-pairs (data not shown). The most abundant repeat elements were DNA transposons, and the most common transposon type was the TcMar-Tc1 transposon-related sequence (24.5%) (Table 1). Unknown elements were also abun- dant and accounted for 19.2% of BES (Table 1). For comparison we masked the rainbow trout BES data- set with the Atlantic salmon repeat database (http://web. uvic.ca/grasp and [37]) and found that only 52.3% of the BES dataset was masked compared to 59.5% with the rainbow trout repeat database. We also estimated the redundancy of each species specific database by repeat- masking the INRA rep1.0 by Salmon Raw 1.6 database Table 1 Characteristics of the INRA RT rep1.0 database Number of elements Percentage of sequence Page 3 of 8 and vice versa. We observed that respectively 35.3% and 52.8% of the databases were masked suggesting differ- ences in the repeats content between the two salmonid species. However, it is also possible that the restriction enzyme selection for the BAC libraries preparation (EcoRI for Atlantic salmon and HindIII for rainbow trout) might have imposed some bias on the repeats content of each database. In addition to the automated detection of repeats using RepeatModeler, we checked for undetected repe- titive elements by aligning the masked BES reads to each other. The alignment results were classified according to the number of significant hits and are summarized in Figure 1. Most of the BES reads (93.4%) had less than 10 hits, indicating that masking with the INRA RT rep1.0 library was effective. How- ever, 711 reads (6.6%) produced more than 10 hits, suggesting that these BES reads may contain repetitive DNA sequences. Moreover, almost 263 reads (2.4%) produced more than 50 hits, suggesting that these BES reads contain interspersed repeats not yet in INRA RT rep1.0 database. Some classes of repeat elements in salmonids can be as long as 1,500 bp [37]. Progress is currently being made to further characterise these long interspersed repeats in rainbow trout by using full length BAC-insert sequencing which will enable characterizing full-length copies of repeat elements and identifying new repeats (Jean-Nicolas Volff, personal communication). Number of elements Percentage of sequence Class I elements LTR retrotransposons LTR/DIRS1 LTR/Gypsy Non-LTR retrotransposons LINE LINE/I LINE/Jockey LINE/L1 LINE/L2 LINE/Penelope LINE/Rex1 SINE SINE/Deu SINE/tRNA-Lys SINE/5S SINE? 2 21 1 1 3 6 19 1 6 5 5 1 1 8 0,02 1,68 0,29 0,01 0,05 0,14 2,18 0,05 3,03 1,09 0,23 0,01 0,01 0,37 Class II elements DNA DNA/Harbinger DNA/hAT DNA/hAT-Charlie DNA/hAT-Tag1 DNA/hAT-Tip100 DNA/Helitron DNA/Maverick DNA/Tc1 DNA/TcMar-Tc1 DNA/TcMar-Tc2 Others elements Simple_repeat rRNA Satellite Unknown elements 1 2 9 5 1 1 1 1 11 46 1 22 3 2 549 0,05 0,02 0,27 0,26 0,05 0,01 0,01 0,01 4,26 24,51 0,01 1,19 0,11 0,06 19,19 Columns 1 and 4 show the name of the repeat elements. Columns 2 and 5 provide the number of repeats elements in the INRA RT rep1.0 generated in this work. Columns 3 and 6 correspond to the percentage of total base pairs masked by the corresponding repeat element.