Research

Analysis of repetitive DNA distribution patterns in the Tribolium castaneum genome

Suzhi Wang¹ , Marcé D Lorenzen² , Richard W Beeman² and Susan J Brown¹

¹Department of Biology, Kansas State University, Manhattan, KS 66506, USA

²Grain Marketing and Production Research Center, Agricultural Research Service, United States Department of Agriculture, College Avenue, Manhattan, KS 66502, USA

author email corresponding author email

Genome Biology 2008, 9:R61doi:10.1186/gb-2008-9-3-r61

Published:	26 March 2008

Subject areas: Genome studies, Bioinformatics

Abstract

Background

Insect genomes vary widely in size, a large fraction of which is often devoted to repetitive DNA. Re-association kinetics indicate that up to 42% of the genome of the red flour beetle, Tribolium castaneum, is repetitive. Analysis of the abundance and distribution of repetitive DNA in the recently sequenced genome of T. castaneum is important for understanding the structure and function of its genome.

Results

Using TRF, TEpipe and RepeatScout we found that approximately 30% of the T. castaneum assembled genome is composed of repetitive DNA. Of this, 17% 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 genome; 65% of these highly repetitive elements and 74% of transposable elements accumulate in regions representing 40% of the assembled genome that is anchored to chromosomes. These regions tend to occur near one end of each chromosome, similar to previously described blocks of pericentric heterochromatin. They contain fewer genes with longer introns, and often correspond with regions of low recombination in the genetic map.

Conclusion

Our study found that transposable elements and other repetitive DNA accumulate in certain regions in the assembled T. castaneum genome. Several lines of evidence suggest these regions are derived from the large blocks of pericentric heterochromatin in T. castaneum chromosomes.