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Landscape and evolutionary dynamics of terminal repeat retrotransposons in miniature in plant genomes

Overview of attention for article published in Genome Biology, January 2016
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  • In the top 25% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (81st percentile)

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Title
Landscape and evolutionary dynamics of terminal repeat retrotransposons in miniature in plant genomes
Published in
Genome Biology, January 2016
DOI 10.1186/s13059-015-0867-y
Pubmed ID
Authors

Dongying Gao, Yupeng Li, Kyung Do Kim, Brian Abernathy, Scott A. Jackson

Abstract

Terminal repeat retrotransposons in miniature (TRIMs) are a unique group of small long terminal repeat retrotransposons that are difficult to identify. Thus far, only a few TRIMs have been characterized in the euphyllophytes, and their evolutionary and biological significance as well as their transposition mechanisms are poorly understood. Using a combination of de novo and homology-based methods, we annotate TRIMs in 48 plant genome sequences, spanning land plants to algae. The TRIMs are grouped into 156 families including 145 that were previously undefined. Notably, we identify the first TRIMs in a lycophyte and non-vascular plants. The majority of the TRIM families are highly conserved and shared within and between plant families. Unlike other long terminal repeat retrotransposons, TRIMs are enriched in or near genes; they are also targeted by sRNAs between 21 and 24 nucleotides in length, and are frequently found in CG body-methylated genes. Importantly, we also identify putative autonomous retrotransposons and very recent transpositions of a TRIM element in Oryza sativa. We perform the most comprehensive analysis of TRIM transposons thus far and report that TRIMs are ubiquitous across plant genomes. Our results show that TRIMs are more frequently associated with large and CG body-methylated genes that have undergone strong purifying selection. Our findings also indicate that TRIMs are likely derived from internal deletions of large long terminal repeat retrotransposons. Finally, our data and methodology are important resources for the characterization and evolutionary and genomic studies of long terminal repeat retrotransposons in other genomes.

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X Demographics

The data shown below were collected from the profiles of 13 X users who shared this research output. Click here to find out more about how the information was compiled.
Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 71 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United Kingdom 1 1%
Chile 1 1%
Czechia 1 1%
France 1 1%
Unknown 67 94%

Demographic breakdown

Readers by professional status Count As %
Researcher 23 32%
Student > Ph. D. Student 11 15%
Student > Master 8 11%
Student > Bachelor 5 7%
Professor > Associate Professor 4 6%
Other 10 14%
Unknown 10 14%
Readers by discipline Count As %
Agricultural and Biological Sciences 33 46%
Biochemistry, Genetics and Molecular Biology 19 27%
Computer Science 2 3%
Nursing and Health Professions 1 1%
Business, Management and Accounting 1 1%
Other 2 3%
Unknown 13 18%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 8. 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 04 March 2016.
All research outputs
#4,688,006
of 25,373,627 outputs
Outputs from Genome Biology
#2,762
of 4,467 outputs
Outputs of similar age
#74,115
of 401,828 outputs
Outputs of similar age from Genome Biology
#53
of 66 outputs
Altmetric has tracked 25,373,627 research outputs across all sources so far. Compared to these this one has done well and is in the 81st percentile: it's in the top 25% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 4,467 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 27.6. This one is in the 38th percentile – i.e., 38% of its peers scored the same or lower than it.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 401,828 tracked outputs that were published within six weeks on either side of this one in any source. This one has done well, scoring higher than 81% of its contemporaries.
We're also able to compare this research output to 66 others from the same source and published within six weeks on either side of this one. This one is in the 19th percentile – i.e., 19% of its contemporaries scored the same or lower than it.