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Planta

, Volume 245, Issue 5, pp 927–938 | Cite as

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

  • Rui Shi
  • Jack P. Wang
  • Ying-Chung Lin
  • Quanzi Li
  • Ying-Hsuan Sun
  • Hao Chen
  • Ronald R. SederoffEmail author
  • Vincent L. ChiangEmail author
Original Article

Abstract

Main conclusion

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.

Keywords

Wood formation Transcriptome Fiber cells Vessel elements Cell wall biosynthesis Co-expression network 

Notes

Acknowledgements

This work was supported by the US National Science Foundation, Plant Genome Research Program Grant DBI-0922391, and the US Department of Energy Grant DE-SC000691. We acknowledge additional supports from the NC State University Jordan Family Distinguished Professor Endowment, the NC State University Forest Biotechnology Industrial Research Consortium, and the National Natural Science Foundation of China (NSFC).

Supplementary material

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Supplementary material 1 (DOCX 50 kb)
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Supplementary material 4 (XLSX 47 kb)

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Copyright information

© Springer-Verlag Berlin Heidelberg 2017

Authors and Affiliations

  • Rui Shi
    • 1
    • 2
  • Jack P. Wang
    • 1
    • 3
  • Ying-Chung Lin
    • 1
    • 3
    • 4
  • Quanzi Li
    • 5
  • Ying-Hsuan Sun
    • 6
  • Hao Chen
    • 1
  • Ronald R. Sederoff
    • 1
    Email author
  • Vincent L. Chiang
    • 1
    • 3
    • 7
    Email author
  1. 1.Forest Biotechnology Group, Department of Forestry and Environmental ResourcesNorth Carolina State UniversityRaleighUSA
  2. 2.Mountain Horticultural Crops Research and Extension Center, Department of HorticultureNorth Carolina State UniversityMills RiverUSA
  3. 3.State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbinChina
  4. 4.Department of Life Sciences, College of Life ScienceNational Taiwan UniversityTaipeiTaiwan
  5. 5.State Key Laboratory of Tree Genetics and BreedingChinese Academy of ForestryBeijingChina
  6. 6.Department of ForestryNational Chung Hsing UniversityTaichungTaiwan
  7. 7.Department of Forest BiomaterialsNorth Carolina State UniversityRaleighUSA

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