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Genome-wide comparison of Asian and African rice reveals high recent activity of DNA transposons.

Type of publication Peer-reviewed
Publikationsform Original article (peer-reviewed)
Author Roffler Stefan, Wicker Thomas,
Project A bioinformatics study to unravel molecular mechanisms that drive genome evolution
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Original article (peer-reviewed)

Journal Mobile DNA
Volume (Issue) 6
Page(s) 8 - 8
Title of proceedings Mobile DNA
DOI 10.1186/s13100-015-0040-x

Abstract

DNA (Class II) transposons are ubiquitous in plant genomes. However, unlike for (Class I) retrotransposons, only little is known about their proliferation mechanisms, activity, and impact on genomes. Asian and African rice (Oryza sativa and O. glaberrima) diverged approximately 600,000 years ago. Their fully sequenced genomes therefore provide an excellent opportunity to study polymorphisms introduced from recent transposon activity. We manually analyzed 1,821 transposon related polymorphisms among which we identified 487 loci which clearly resulted from DNA transposon insertions and excisions. In total, we estimate about 4,000 (3.5% of all DNA transposons) to be polymorphic between the two species, indicating a high level of transposable element (TE) activity. The vast majority of the recently active elements are non-autonomous. Nevertheless, we identified multiple potentially functional autonomous elements. Furthermore, we quantified the impacts of insertions and excisions on the adjacent sequences. Transposon insertions were found to be generally precise, creating simple target site duplications. In contrast, excisions almost always go along with the deletion of flanking sequences and/or the insertion of foreign 'filler' segments. Some of the excision-triggered deletions ranged from hundreds to thousands of bp flanking the excision site. Furthermore, we found in some superfamilies unexpectedly low numbers of excisions. This suggests that some excisions might cause such large-scale rearrangements so that they cannot be detected anymore. We conclude that the activity of DNA transposons (particularly the excision process) is a major evolutionary force driving the generation of genetic diversity.
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