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Tissue and cell-type co-expression networks of transcription factors and wood component genes in Populus trichocarpa

Overview of attention for article published in Planta, January 2017
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Title
Tissue and cell-type co-expression networks of transcription factors and wood component genes in Populus trichocarpa
Published in
Planta, January 2017
DOI 10.1007/s00425-016-2640-1
Pubmed ID
Authors

Rui Shi, Jack P. Wang, Ying-Chung Lin, Quanzi Li, Ying-Hsuan Sun, Hao Chen, Ronald R. Sederoff, Vincent L. Chiang

Abstract

Co-expression networks based on transcriptomes of Populus trichocarpa major tissues and specific cell types suggest redundant control of cell wall component biosynthetic genes by transcription factors in wood formation. We analyzed the transcriptomes of five tissues (xylem, phloem, shoot, leaf, and root) and two wood forming cell types (fiber and vessel) of Populus trichocarpa to assemble gene co-expression subnetworks associated with wood formation. We identified 165 transcription factors (TFs) that showed xylem-, fiber-, and vessel-specific expression. Of these 165 TFs, 101 co-expressed (correlation coefficient, r > 0.7) with the 45 secondary cell wall cellulose, hemicellulose, and lignin biosynthetic genes. Each cell wall component gene co-expressed on average with 34 TFs, suggesting redundant control of the cell wall component gene expression. Co-expression analysis showed that the 101 TFs and the 45 cell wall component genes each has two distinct groups (groups 1 and 2), based on their co-expression patterns. The group 1 TFs (44 members) are predominantly xylem and fiber specific, and are all highly positively co-expressed with the group 1 cell wall component genes (30 members), suggesting their roles as major wood formation regulators. Group 1 TFs include a lateral organ boundary domain gene (LBD) that has the highest number of positively correlated cell wall component genes (36) and TFs (47). The group 2 TFs have 57 members, including 14 vessel-specific TFs, and are generally less correlated with the cell wall component genes. An exception is a vessel-specific basic helix-loop-helix (bHLH) gene that negatively correlates with 20 cell wall component genes, and may function as a key transcriptional suppressor. The co-expression networks revealed here suggest a well-structured transcriptional homeostasis for cell wall component biosynthesis during wood formation.

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Mendeley readers

The data shown below were compiled from readership statistics for 39 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 39 100%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 13 33%
Student > Master 5 13%
Unspecified 4 10%
Researcher 4 10%
Professor > Associate Professor 4 10%
Other 9 23%
Readers by discipline Count As %
Agricultural and Biological Sciences 22 56%
Biochemistry, Genetics and Molecular Biology 10 26%
Unspecified 6 15%
Chemical Engineering 1 3%

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 23 May 2017.
All research outputs
#9,766,532
of 12,221,286 outputs
Outputs from Planta
#1,414
of 1,785 outputs
Outputs of similar age
#233,529
of 331,888 outputs
Outputs of similar age from Planta
#18
of 29 outputs
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