Dataset Information

How repetitive are genomes?

ABSTRACT:

Background

Genome sequences vary strongly in their repetitiveness and the causes for this are still debated. Here we propose a novel measure of genome repetitiveness, the index of repetitiveness, Ir, which can be computed in time proportional to the length of the sequences analyzed. We apply it to 336 genomes from all three domains of life.

Results

The expected value of Ir is zero for random sequences of any G/C content and greater than zero for sequences with excess repeats. We find that the Ir of archaea is significantly smaller than that of eubacteria, which in turn is smaller than that of eukaryotes. Mouse chromosomes have a significantly higher Ir than human chromosomes and within each genome the Y chromosome is most repetitive. A sliding window analysis reveals that the human HOXA cluster and two surrounding genes are characterized by local minima in Ir. A program for calculating the Ir is freely available at http://adenine.biz.fh-weihenstephan.de/ir/.

Conclusion

The general measure of DNA repetitiveness proposed in this paper can be efficiently computed on a genomic scale. This reveals a broad spectrum of repetitiveness among diverse genomes which agrees qualitatively with previous studies of repeat content. A sliding window analysis helps to analyze the intragenomic distribution of repeats.

SUBMITTER: Haubold B

PROVIDER: S-EPMC1769404 | biostudies-literature | 2006 Dec

REPOSITORIES: biostudies-literature

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Publications

How repetitive are genomes?

Haubold Bernhard B Wiehe Thomas T

BMC bioinformatics 20061222

<h4>Background</h4>Genome sequences vary strongly in their repetitiveness and the causes for this are still debated. Here we propose a novel measure of genome repetitiveness, the index of repetitiveness, Ir, which can be computed in time proportional to the length of the sequences analyzed. We apply it to 336 genomes from all three domains of life.<h4>Results</h4>The expected value of Ir is zero for random sequences of any G/C content and greater than zero for sequences with excess repeats. We f ...[more]

PMID: 17187668

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Project description:BackgroundSome clover species, particularly Trifolium subterraneum, have previously been reported to have highly unusual plastomes, relative to closely related legumes, enlarged with many duplications, gene losses and the presence of DNA unique to Trifolium, which may represent horizontal transfer. In order to pinpoint the evolutionary origin of this phenomenon within the genus Trifolium, we sequenced and assembled the plastomes of eight additional Trifolium species widely sampled from across the genus.ResultsThe Trifolium plastomes fell into two groups: those of Trifolium boissieri, T. strictum and T. glanduliferum (representing subgenus Chronosemium and subg. Trifolium section Paramesus) were tractable, assembled readily and were not unusual in the general context of Fabeae plastomes. The other Trifolium species ("core Trifolium") proved refractory to assembly mainly because of numerous short duplications. These species form a single clade, which we call the "refractory clade" (comprising subg, Trifolium sections Lupinaster, Trifolium, Trichocephalum, Vesicastrum and Trifoliastrum). The characteristics of the refractory clade are the presence of numerous short duplications and 7-15% longer genomes than the tractable species. Molecular dating estimates that the origin of the most recent common ancestor (MRCA) of the refractory clade is approximately 13.1 million years ago (MYA). This is considerably younger than the estimated MRCA ages of Trifolium (c. 18.6 MYA) and Trifolium subg. Trifolium (16.1 MYA).ConclusionsWe conclude that the unusual repetitive plastome type previously characterized in Trifolium subterraneum had a single origin within Trifolium and is characteristic of most (but not all) species of subgenus Trifolium. It appears that an ancestral plastome within Trifolium underwent an evolutionary change resulting in plastomes that either actively promoted, were permissive to, or were unable to control, duplications within the genome. The precise mechanism of this important change in the mode and tempo of plastome evolution deserves further investigation.

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How repetitive are genomes?

Background

Results

Conclusion

Publications

How repetitive are genomes?

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