title: Tissue and cell-type co-expression networks of transcription factors and wood component genes in Populus trichocarpa.
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.
authors.affiliation: Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, 27695, USA.|Mountain Horticultural Crops Research and Extension Center, Department of Horticulture, North Carolina State University, Mills River, NC, 28759, USA.
authors.forename: Rui
authors.initials: R
authors.lastname: Shi
authors.affiliation: Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, 27695, USA.|State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China.
authors.forename: Jack P
authors.initials: JP
authors.lastname: Wang
authors.affiliation: Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, 27695, USA.|State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China.|Department of Life Sciences, College of Life Science, National Taiwan University, Taipei, 10617, Taiwan.
authors.forename: Ying-Chung
authors.initials: YC
authors.lastname: Lin
authors.affiliation: State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China.
authors.forename: Quanzi
authors.initials: Q
authors.lastname: Li
authors.affiliation: Department of Forestry, National Chung Hsing University, Taichung, 40227, Taiwan.
authors.forename: Ying-Hsuan
authors.initials: YH
authors.lastname: Sun
authors.affiliation: Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, 27695, USA.
authors.forename: Hao
authors.initials: H
authors.lastname: Chen
authors.affiliation: Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, 27695, USA. ron_sederoff@ncsu.edu.
authors.forename: Ronald R
authors.initials: RR
authors.lastname: Sederoff
authors.affiliation: Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, 27695, USA. vchiang@ncsu.edu.|State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China. vchiang@ncsu.edu.|Department of Forest Biomaterials, North Carolina State University, Raleigh, NC, 27695, USA. vchiang@ncsu.edu.
authors.forename: Vincent L
authors.initials: VL
authors.lastname: Chiang
mesh_terms: D002473:Cell Wall / Q000378:metabolism; D002482:Cellulose / Q000378:metabolism; D016000:Cluster Analysis; D018506:Gene Expression Regulation, Plant; D008031:Lignin / Q000378:metabolism; D058977:Molecular Sequence Annotation; D009928:Organ Specificity; D052585:Phloem / Q000235:genetics / Q000254:growth & development; D018515:Plant Leaves / Q000235:genetics / Q000254:growth & development; D010940:Plant Proteins / Q000235:genetics*; D032107:Populus / Q000235:genetics* / Q000254:growth & development; D017423:Sequence Analysis, RNA; D014157:Transcription Factors / Q000235:genetics; D059467:Transcriptome; D014934:Wood / Q000235:genetics* / Q000254:growth & development; D052584:Xylem / Q000235:genetics / Q000254:growth & development
chemical_list: D010940:Plant Proteins; D014157:Transcription Factors; D002482:Cellulose; D008031:Lignin
keywords: Cell wall biosynthesis; Co-expression network; Fiber cells; Transcriptome; Vessel elements; Wood formation