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A new look at the LTR retrotransposon content of the chicken genome

Overview of attention for article published in BMC Genomics, August 2016
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  • Good Attention Score compared to outputs of the same age (71st percentile)
  • Good Attention Score compared to outputs of the same age and source (76th percentile)

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10 tweeters

Citations

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31 Dimensions

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31 Mendeley
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Title
A new look at the LTR retrotransposon content of the chicken genome
Published in
BMC Genomics, August 2016
DOI 10.1186/s12864-016-3043-1
Pubmed ID
Authors

Andrew S. Mason, Janet E. Fulton, Paul M. Hocking, David W. Burt

Abstract

LTR retrotransposons contribute approximately 10 % of the mammalian genome, but it has been previously reported that there is a deficit of these elements in the chicken relative to both mammals and other birds. A novel LTR retrotransposon classification pipeline, LocaTR, was developed and subsequently utilised to re-examine the chicken LTR retrotransposon annotation, and determine if the proposed chicken deficit is biologically accurate or simply a technical artefact. Using LocaTR 3.01 % of the chicken galGal4 genome assembly was annotated as LTR retrotransposon-derived elements (nearly double the previous annotation), including 1,073 that were structurally intact. Element distribution is significantly correlated with chromosome size and is non-random within each chromosome. Elements are significantly depleted within coding regions and enriched in gene sparse areas of the genome. Over 40 % of intact elements are found in clusters, unrelated by age or genera, generally in poorly recombining regions. The transcription of most LTR retrotransposons were suppressed or incomplete, but individual domain and full length retroviral transcripts were produced in some cases, although mostly with regularly interspersed stop codons in all reading frames. Furthermore, RNAseq data from 23 diverse tissues enabled greater characterisation of the co-opted endogenous retrovirus Ovex1. This gene was shown to be expressed ubiquitously but at variable levels across different tissues. LTR retrotransposon content was found to be very variable across the avian lineage and did not correlate with either genome size or phylogenetic position. However, the extent of previous, species-specific LTR retrotransposon annotation appears to be a confounding factor. Use of the novel LocaTR pipeline has nearly doubled the annotated LTR retrotransposon content of the chicken genome compared to previous estimates. Further analysis has described element distribution, clustering patterns and degree of expression in a variety of adult tissues, as well as in three embryonic stages. This study also enabled better characterisation of the co-opted gamma retroviral envelope gene Ovex1. Additionally, this work suggests that there is no deficit of LTR retrotransposons within the Galliformes relative to other birds, or to mammalian genomes when scaled for the three-fold difference in genome size.

Twitter Demographics

The data shown below were collected from the profiles of 10 tweeters who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 31 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Canada 1 3%
Unknown 30 97%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 6 19%
Student > Bachelor 6 19%
Student > Master 5 16%
Student > Doctoral Student 3 10%
Researcher 3 10%
Other 5 16%
Unknown 3 10%
Readers by discipline Count As %
Agricultural and Biological Sciences 11 35%
Biochemistry, Genetics and Molecular Biology 10 32%
Mathematics 1 3%
Veterinary Science and Veterinary Medicine 1 3%
Economics, Econometrics and Finance 1 3%
Other 3 10%
Unknown 4 13%

Attention Score in Context

This research output has an Altmetric Attention Score of 5. 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 19 May 2020.
All research outputs
#5,338,429
of 20,275,020 outputs
Outputs from BMC Genomics
#2,325
of 9,985 outputs
Outputs of similar age
#80,016
of 283,261 outputs
Outputs of similar age from BMC Genomics
#13
of 52 outputs
Altmetric has tracked 20,275,020 research outputs across all sources so far. This one has received more attention than most of these and is in the 73rd percentile.
So far Altmetric has tracked 9,985 research outputs from this source. They receive a mean Attention Score of 4.5. This one has done well, scoring higher than 76% of its peers.
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 283,261 tracked outputs that were published within six weeks on either side of this one in any source. This one has gotten more attention than average, scoring higher than 71% of its contemporaries.
We're also able to compare this research output to 52 others from the same source and published within six weeks on either side of this one. This one has done well, scoring higher than 76% of its contemporaries.