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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.

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Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 56 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Argentina 1 2%
Unknown 55 98%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 12 21%
Student > Bachelor 6 11%
Student > Master 6 11%
Researcher 5 9%
Student > Postgraduate 4 7%
Other 9 16%
Unknown 14 25%
Readers by discipline Count As %
Agricultural and Biological Sciences 29 52%
Biochemistry, Genetics and Molecular Biology 4 7%
Computer Science 2 4%
Arts and Humanities 1 2%
Environmental Science 1 2%
Other 1 2%
Unknown 18 32%
Attention Score in Context

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
#15,349,796
of 22,832,057 outputs
Outputs from BMC Genomics
#6,694
of 10,655 outputs
Outputs of similar age
#166,455
of 284,824 outputs
Outputs of similar age from BMC Genomics
#292
of 393 outputs
Altmetric has tracked 22,832,057 research outputs across all sources so far. This one is in the 22nd percentile – i.e., 22% of other outputs scored the same or lower than it.
So far Altmetric has tracked 10,655 research outputs from this source. They receive a mean Attention Score of 4.7. This one is in the 29th percentile – i.e., 29% of its peers scored the same or lower than it.
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