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Identification and analysis of unitary loss of long-established protein-coding genes in Poaceae shows evidences for biased gene loss and putatively functional transcription of relics

Overview of attention for article published in BMC Evolutionary Biology, April 2015
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  • Above-average Attention Score compared to outputs of the same age (54th percentile)

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Citations

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Title
Identification and analysis of unitary loss of long-established protein-coding genes in Poaceae shows evidences for biased gene loss and putatively functional transcription of relics
Published in
BMC Evolutionary Biology, April 2015
DOI 10.1186/s12862-015-0345-x
Pubmed ID
Authors

Yi Zhao, Liang Tang, Zhe Li, Jinpu Jin, Jingchu Luo, Ge Gao

Abstract

Long-established protein-coding genes may lose their coding potential during evolution ("unitary gene loss"). Members of the Poaceae family are a major food source and represent an ideal model clade for plant evolution research. However, the global pattern of unitary gene loss in Poaceae genomes as well as the evolutionary fate of lost genes are still less-investigated and remain largely elusive. Using a locally developed pipeline, we identified 129 unitary gene loss events for long-established protein-coding genes from four representative species of Poaceae, i.e. brachypodium, rice, sorghum and maize. Functional annotation suggested that the lost genes in all or most of Poaceae species are enriched for genes involved in development and response to endogenous stimulus. We also found that 44 mutated genomic loci of lost genes, which we referred as relics, were still actively transcribed, and of which 84% (37 of 44) showed significantly differential expression across different tissues. More interestingly, we found that there were totally five expressed relics may function as competitive endogenous RNA in brachypodium, rice and sorghum genome. Based on comparative genomics and transcriptome data, we firstly compiled a comprehensive catalogue of unitary gene loss events in Poaceae species and characterized a statistically significant functional preference for these lost genes as well showed the potential of relics functioning as competitive endogenous RNAs in Poaceae genomes.

Twitter Demographics

The data shown below were collected from the profiles of 3 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 18 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 18 100%

Demographic breakdown

Readers by professional status Count As %
Researcher 5 28%
Student > Doctoral Student 3 17%
Student > Ph. D. Student 3 17%
Student > Postgraduate 2 11%
Student > Bachelor 2 11%
Other 1 6%
Unknown 2 11%
Readers by discipline Count As %
Agricultural and Biological Sciences 11 61%
Biochemistry, Genetics and Molecular Biology 3 17%
Materials Science 1 6%
Unknown 3 17%

Attention Score in Context

This research output has an Altmetric Attention Score of 2. 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 28 August 2015.
All research outputs
#10,065,824
of 17,829,175 outputs
Outputs from BMC Evolutionary Biology
#1,861
of 2,801 outputs
Outputs of similar age
#104,445
of 237,216 outputs
Outputs of similar age from BMC Evolutionary Biology
#1
of 1 outputs
Altmetric has tracked 17,829,175 research outputs across all sources so far. This one is in the 42nd percentile – i.e., 42% of other outputs scored the same or lower than it.
So far Altmetric has tracked 2,801 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 10.8. This one is in the 31st percentile – i.e., 31% 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 237,216 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 54% of its contemporaries.
We're also able to compare this research output to 1 others from the same source and published within six weeks on either side of this one. This one has scored higher than all of them