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The WRKY transcription factor family and senescence in switchgrass

Overview of attention for article published in BMC Genomics, November 2015
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Title
The WRKY transcription factor family and senescence in switchgrass
Published in
BMC Genomics, November 2015
DOI 10.1186/s12864-015-2057-4
Pubmed ID
Authors

Charles I. Rinerson, Erin D. Scully, Nathan A. Palmer, Teresa Donze-Reiner, Roel C. Rabara, Prateek Tripathi, Qingxi J Shen, Scott E. Sattler, Jai S. Rohila, Gautam Sarath, Paul J. Rushton

Abstract

Early aerial senescence in switchgrass (Panicum virgatum) can significantly limit biomass yields. WRKY transcription factors that can regulate senescence could be used to reprogram senescence and enhance biomass yields. All potential WRKY genes present in the version 1.0 of the switchgrass genome were identified and curated using manual and bioinformatic methods. Expression profiles of WRKY genes in switchgrass flag leaf RNA-Seq datasets were analyzed using clustering and network analyses tools to identify both WRKY and WRKY-associated gene co-expression networks during leaf development and senescence onset. We identified 240 switchgrass WRKY genes including members of the RW5 and RW6 families of resistance proteins. Weighted gene co-expression network analysis of the flag leaf transcriptomes across development readily separated clusters of co-expressed genes into thirteen modules. A visualization highlighted separation of modules associated with the early and senescence-onset phases of flag leaf growth. The senescence-associated module contained 3000 genes including 23 WRKYs. Putative promoter regions of senescence-associated WRKY genes contained several cis-element-like sequences suggestive of responsiveness to both senescence and stress signaling pathways. A phylogenetic comparison of senescence-associated WRKY genes from switchgrass flag leaf with senescence-associated WRKY genes from other plants revealed notable hotspots in Group I, IIb, and IIe of the phylogenetic tree. We have identified and named 240 WRKY genes in the switchgrass genome. Twenty three of these genes show elevated mRNA levels during the onset of flag leaf senescence. Eleven of the WRKY genes were found in hotspots of related senescence-associated genes from multiple species and thus represent promising targets for future switchgrass genetic improvement. Overall, individual WRKY gene expression profiles could be readily linked to developmental stages of flag leaves.

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 44 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Argentina 1 2%
Unknown 43 98%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 12 27%
Student > Master 5 11%
Student > Bachelor 5 11%
Student > Postgraduate 4 9%
Researcher 4 9%
Other 7 16%
Unknown 7 16%
Readers by discipline Count As %
Agricultural and Biological Sciences 27 61%
Biochemistry, Genetics and Molecular Biology 3 7%
Arts and Humanities 1 2%
Environmental Science 1 2%
Computer Science 1 2%
Other 1 2%
Unknown 10 23%

Attention Score in Context

This research output has an Altmetric Attention Score of 1. 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 11 November 2015.
All research outputs
#10,647,130
of 16,638,522 outputs
Outputs from BMC Genomics
#5,614
of 9,107 outputs
Outputs of similar age
#158,812
of 288,051 outputs
Outputs of similar age from BMC Genomics
#725
of 996 outputs
Altmetric has tracked 16,638,522 research outputs across all sources so far. This one is in the 23rd percentile – i.e., 23% of other outputs scored the same or lower than it.
So far Altmetric has tracked 9,107 research outputs from this source. They receive a mean Attention Score of 4.3. This one is in the 30th percentile – i.e., 30% of its peers scored the same or lower than it.
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We're also able to compare this research output to 996 others from the same source and published within six weeks on either side of this one. This one is in the 20th percentile – i.e., 20% of its contemporaries scored the same or lower than it.