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Both mechanism and age of duplications contribute to biased gene retention patterns in plants

Overview of attention for article published in BMC Genomics, January 2017
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Title
Both mechanism and age of duplications contribute to biased gene retention patterns in plants
Published in
BMC Genomics, January 2017
DOI 10.1186/s12864-016-3423-6
Pubmed ID
Authors

Hugo V. S. Rody, Gregory J. Baute, Loren H. Rieseberg, Luiz O. Oliveira

Abstract

All extant seed plants are successful paleopolyploids, whose genomes carry duplicate genes that have survived repeated episodes of diploidization. However, the survival of gene duplicates is biased with respect to gene function and mechanism of duplication. Transcription factors, in particular, are reported to be preferentially retained following whole-genome duplications (WGDs), but disproportionately lost when duplicated by tandem events. An explanation for this pattern is provided by the Gene Balance Hypothesis (GBH), which posits that duplicates of highly connected genes are retained following WGDs to maintain optimal stoichiometry among gene products; but such connected gene duplicates are disfavored following tandem duplications. We used genomic data from 25 taxonomically diverse plant species to investigate the roles of duplication mechanism, gene function, and age of duplication in the retention of duplicate genes. Enrichment analyses were conducted to identify Gene Ontology (GO) functional categories that were overrepresented in either WGD or tandem duplications, or across ranges of divergence times. Tandem paralogs were much younger, on average, than WGD paralogs and the most frequently overrepresented GO categories were not shared between tandem and WGD paralogs. Transcription factors were overrepresented among ancient paralogs regardless of mechanism of origin or presence of a WGD. Also, in many cases, there was no bias toward transcription factor retention following recent WGDs. Both the fixation and the retention of duplicated genes in plant genomes are context-dependent events. The strong bias toward ancient transcription factor duplicates can be reconciled with the GBH if selection for optimal stoichiometry among gene products is strongest following the earliest polyploidization events and becomes increasingly relaxed as gene families expand.

Twitter Demographics

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Mendeley readers

The data shown below were compiled from readership statistics for 27 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 2 7%
Unknown 25 93%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 7 26%
Student > Bachelor 6 22%
Student > Postgraduate 4 15%
Researcher 3 11%
Unspecified 3 11%
Other 4 15%
Readers by discipline Count As %
Agricultural and Biological Sciences 12 44%
Biochemistry, Genetics and Molecular Biology 8 30%
Unspecified 6 22%
Computer Science 1 4%

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 24 February 2017.
All research outputs
#6,492,044
of 11,340,713 outputs
Outputs from BMC Genomics
#3,666
of 6,795 outputs
Outputs of similar age
#150,008
of 316,768 outputs
Outputs of similar age from BMC Genomics
#95
of 187 outputs
Altmetric has tracked 11,340,713 research outputs across all sources so far. This one is in the 40th percentile – i.e., 40% of other outputs scored the same or lower than it.
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