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Title: Analysis of repetitive DNA distribution patterns in the Tribolium castaneum genome

Author
item WANG, SUZHI - KANSAS STATE UNIVERSITY
item Lorenzen, Marce
item Beeman, Richard
item BROWN, SUSAN - KANSAS STATE UNIVERSITY

Submitted to: Genome Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/26/2008
Publication Date: 3/26/2008
Citation: Wang, S., Lorenzen, M.D., Beeman, R.W., Brown, S.J. 2008. Analysis of repetitive DNA distribution patterns in the Tribolium castaneum genome. Genome Biology 9: R61 (14 pages).

Interpretive Summary: Most insects have about the same total number of genes (about 15,000), but the total sizes of their genomes can vary by a factor of more than 100. This is because genes themselves represent only a small fraction of the total DNA in an insect’s chromosomes. Much of the DNA has unknown function or consists of many copies of repeated sequences. We analyzed the types and chromosomal distribution of this repetitive DNA in the red flour beetle, and found that it comprises almost half of the total DNA on the chromosomes. Understanding this “gene-poor” component of insect DNA will help us understand the function of adjacent “gene-rich” regions, which in turn will lead to a better understanding of many important aspects of insect biology.

Technical Abstract: Insect genomes vary widely in size, in part because of a sometimes large and variable repetitive DNA component. Prior to the determination of the genome sequence of the red flour beetle Tribolium castaneum, reassociation kinetics had indicated that up to 42% of this genome is composed of repetitive sequences (Brown, 90). Using TRF, TEpipe and RepeatScout we found that approximately 30% of the Tribolium castaneum assembled 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 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 linkage groups. These regions tend to occur near one end of each linkage group, 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. Analysis of the abundance and distribution of repetitive DNA in T. castaneum will contribute to our understanding of the structure and function of this genome.