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X Demographics
Mendeley readers
Attention Score in Context
| Title |
DNA methylation changes facilitated evolution of genes derived from Mutator-like transposable elements
|
|---|---|
| Published in |
Genome Biology, May 2016
|
| DOI | 10.1186/s13059-016-0954-8 |
| Pubmed ID | |
| Authors |
Jun Wang, Yeisoo Yu, Feng Tao, Jianwei Zhang, Dario Copetti, Dave Kudrna, Jayson Talag, Seunghee Lee, Rod A. Wing, Chuanzhu Fan |
| Abstract |
Mutator-like transposable elements, a class of DNA transposons, exist pervasively in both prokaryotic and eukaryotic genomes, with more than 10,000 copies identified in the rice genome. These elements can capture ectopic genomic sequences that lead to the formation of new gene structures. Here, based on whole-genome comparative analyses, we comprehensively investigated processes and mechanisms of the evolution of putative genes derived from Mutator-like transposable elements in ten Oryza species and the outgroup Leersia perieri, bridging ~20 million years of evolutionary history. Our analysis identified thousands of putative genes in each of the Oryza species, a large proportion of which have evidence of expression and contain chimeric structures. Consistent with previous reports, we observe that the putative Mutator-like transposable element-derived genes are generally GC-rich and mainly derive from GC-rich parental sequences. Furthermore, we determine that Mutator-like transposable elements capture parental sequences preferentially from genomic regions with low methylation levels and high recombination rates. We explicitly show that methylation levels in the internal and terminated inverted repeat regions of these elements, which might be directed by the 24-nucleotide small RNA-mediated pathway, are different and change dynamically over evolutionary time. Lastly, we demonstrate that putative genes derived from Mutator-like transposable elements tend to be expressed in mature pollen, which have undergone de-methylation programming, thereby providing a permissive expression environment for newly formed/transposable element-derived genes. Our results suggest that DNA methylation may be a primary mechanism to facilitate the origination, survival, and regulation of genes derived from Mutator-like transposable elements, thus contributing to the evolution of gene innovation and novelty in plant genomes. |
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.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| United Kingdom | 2 | 15% |
| Spain | 1 | 8% |
| United States | 1 | 8% |
| Brazil | 1 | 8% |
| Saudi Arabia | 1 | 8% |
| France | 1 | 8% |
| Unknown | 6 | 46% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Members of the public | 7 | 54% |
| Scientists | 4 | 31% |
| Practitioners (doctors, other healthcare professionals) | 1 | 8% |
| Science communicators (journalists, bloggers, editors) | 1 | 8% |
Mendeley readers
The data shown below were compiled from readership statistics for 69 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| United States | 2 | 3% |
| Japan | 1 | 1% |
| France | 1 | 1% |
| Brazil | 1 | 1% |
| Unknown | 64 | 93% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Student > Ph. D. Student | 19 | 28% |
| Researcher | 17 | 25% |
| Student > Master | 9 | 13% |
| Student > Bachelor | 5 | 7% |
| Professor | 3 | 4% |
| Other | 6 | 9% |
| Unknown | 10 | 14% |
| Readers by discipline | Count | As % |
|---|---|---|
| Agricultural and Biological Sciences | 35 | 51% |
| Biochemistry, Genetics and Molecular Biology | 15 | 22% |
| Computer Science | 3 | 4% |
| Engineering | 2 | 3% |
| Social Sciences | 1 | 1% |
| Other | 1 | 1% |
| Unknown | 12 | 17% |
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 26 June 2017.
All research outputs
#4,823,998
of 25,373,627 outputs
Outputs from Genome Biology
#2,798
of 4,467 outputs
Outputs of similar age
#70,226
of 312,371 outputs
Outputs of similar age from Genome Biology
#59
of 77 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 80th 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 37th percentile – i.e., 37% 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 312,371 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 77% of its contemporaries.
We're also able to compare this research output to 77 others from the same source and published within six weeks on either side of this one. This one is in the 23rd percentile – i.e., 23% of its contemporaries scored the same or lower than it.