Analysis of repetitive DNA distribution patterns in the Tribolium castaneum genome

Background Insect genomes vary widely in size, due in part to a sometimes large and variable repetitive DNA component. Reassociation kinetics indicate that up to 42% of the genome of the red flour beetle Tribolium castaneum, is composed of repetitive sequences. Analysis of the abundance and distribution of repetitive DNA in the recently-sequenced genome of T. castaneum will contribute to our understanding of the structure and function of this genome. Results Using TandomRepeatFinder, TEpipe and RepeatScout we found that approximately 30% of the assembled Tribolium genome is composed of repetitive DNA. 17% of the repetitive DNA is found in tandem arrays and the remaining 83% is dispersed, including transposable elements, which in themselves constitute 5-6% of the genome. RepeatScout identified 31 highly repetitive DNA elements with repeat units longer than 100-bp, which constitute 7% of the assembled genome. 65% of these highly repetitive elements and 74% of transposable elements accumulate in regions representing 40% of the assembled and anchored genome. These regions are centrally clustered in the longest chromosome build and occur near one end of each of the remaining chromosome builds, similar to previously described blocks of pericentric heterochromatin. They also contain fewer genes with longer introns, and often correspond to regions of low recombination in the genetic map. Conclusion Almost 30% of the Tribolium genome assembly is composed of transposable elements and other types of repetitive DNA that accumulate in regions likely to represent the large blocks of pericentric heterochromatin in Tribolium chromosomes.