Repeat structure of the catfish genome:: a genomic and transcriptomic assessment of Tc1-like transposon elements in channel catfish (Ictalurus punctatus)

We have assessed the distribution and diversity of members of the Tcllmariner superfamily of transposable elements in the channel catfish (Ictalurus punctatus) genome as well as evaluating the extent of transcription of Tcl transposases in the species. Through use of PCR amplification and sequencing, assessment of random BAC end sequences (BES) equivalent to 1.2% genome coverage, and screening of over 45,000 catfish ESTs, a significant proportion of Tcl-like elements and their associated transcripts were captured. Up to 4.2% of the catfish genome in base pairs appears to be composed of Tcl-like transposon-related sequences and a significant fraction of the catfish cellular mRNA, approximately 0.6%, was transcribed from transposon-related sequences in both sense and antisense orientations. Based on results of repeat-masking, as much as 10% of BAC end sequences from catfish, which is a random survey of the genome, contain some remnant of Tcl elements, suggesting that these elements are present in the catfish genome as numerous, small remnants of the transposons. Phylogenetic analysis allowed comparison of catfish Tcl transposase types with those found in other vertebrate and invertebrate species. In spite of the existence of many types of Tcl-like sequences that are not yet able to be placed in clades with strong statistical support, it is clear that multiple families of Tcl-like elements exist in channel catfish.