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

Overview of attention for article published in Mobile DNA, April 2015
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  • In the top 25% of all research outputs scored by Altmetric
  • Good Attention Score compared to outputs of the same age (75th percentile)

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10 tweeters
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1 Google+ user

Citations

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7 Dimensions

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50 Mendeley
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Title
Genome-wide comparison of Asian and African rice reveals high recent activity of DNA transposons
Published in
Mobile DNA, April 2015
DOI 10.1186/s13100-015-0040-x
Pubmed ID
Authors

Stefan Roffler, Thomas Wicker

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.

Twitter Demographics

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Mendeley readers

The data shown below were compiled from readership statistics for 50 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Brazil 2 4%
Italy 1 2%
France 1 2%
Netherlands 1 2%
United States 1 2%
Philippines 1 2%
Unknown 43 86%

Demographic breakdown

Readers by professional status Count As %
Researcher 19 38%
Student > Ph. D. Student 10 20%
Student > Doctoral Student 4 8%
Lecturer 2 4%
Student > Master 2 4%
Other 6 12%
Unknown 7 14%
Readers by discipline Count As %
Agricultural and Biological Sciences 32 64%
Biochemistry, Genetics and Molecular Biology 7 14%
Nursing and Health Professions 1 2%
Computer Science 1 2%
Chemistry 1 2%
Other 0 0%
Unknown 8 16%

Attention Score in Context

This research output has an Altmetric Attention Score of 6. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 09 May 2015.
All research outputs
#4,918,083
of 20,032,353 outputs
Outputs from Mobile DNA
#106
of 307 outputs
Outputs of similar age
#59,453
of 241,712 outputs
Outputs of similar age from Mobile DNA
#1
of 1 outputs
Altmetric has tracked 20,032,353 research outputs across all sources so far. Compared to these this one has done well and is in the 75th percentile: it's in the top 25% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 307 research outputs from this source. They typically receive a little more attention than average, with a mean Attention Score of 6.6. This one has gotten more attention than average, scoring higher than 64% of its peers.
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