Limits...
Analysis of repetitive DNA distribution patterns in the Tribolium castaneum genome.

Wang S, Lorenzen MD, Beeman RW, Brown SJ - Genome Biol. (2008)

Bottom Line: 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.Our study found that transposable elements and other repetitive DNA accumulate in certain regions in the assembled T. castaneum genome.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biology, Kansas State University, Manhattan, KS 66506, USA. suzyi@gmail.com

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.

Show MeSH
Distribution of microsatellites, minisatellites and satellites on each chromosome of the T. castaneum genome.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2397513&req=5

Figure 1: Distribution of microsatellites, minisatellites and satellites on each chromosome of the T. castaneum genome.

Mentions: In Tribolium, micro- and minisatellites are evenly distributed between chromosomes, including the concatenated group of unmapped scaffolds, but certain chromosomes contain more long satellites (>100 bp) than others (Figure 1). Such variability may reflect real differences in the organizational structure of each chromosome or it might simply be an artifact caused by the assembly status of the genome, especially in light of the large number of scaffolds containing long satellites that lack chromosome assignments.


Analysis of repetitive DNA distribution patterns in the Tribolium castaneum genome.

Wang S, Lorenzen MD, Beeman RW, Brown SJ - Genome Biol. (2008)

Distribution of microsatellites, minisatellites and satellites on each chromosome of the T. castaneum genome.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2397513&req=5

Figure 1: Distribution of microsatellites, minisatellites and satellites on each chromosome of the T. castaneum genome.
Mentions: In Tribolium, micro- and minisatellites are evenly distributed between chromosomes, including the concatenated group of unmapped scaffolds, but certain chromosomes contain more long satellites (>100 bp) than others (Figure 1). Such variability may reflect real differences in the organizational structure of each chromosome or it might simply be an artifact caused by the assembly status of the genome, especially in light of the large number of scaffolds containing long satellites that lack chromosome assignments.

Bottom Line: 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.Our study found that transposable elements and other repetitive DNA accumulate in certain regions in the assembled T. castaneum genome.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biology, Kansas State University, Manhattan, KS 66506, USA. suzyi@gmail.com

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.

Show MeSH