文献类型：期刊文献

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

作者：Shi, Rui[1,2] Wang, Jack P.[1,3] Lin, Ying-Chung[1,3,4] Li, Quanzi[5] Sun, Ying-Hsuan[6] Chen, Hao[1] Sederoff, Ronald R.[1] Chiang, Vincent L.[1,3,7]

第一作者：Shi, Rui

通信作者：Sederoff, RR[1];Chiang, VL[1];Chiang, VL[2];Chiang, VL[3]

机构：[1]North Carolina State Univ, Dept Forestry & Environm Resources, Forest Biotechnol Grp, Raleigh, NC 27695 USA;[2]North Carolina State Univ, Dept Hort, Mt Hort Crops Res & Extens Ctr, Mills River, NC 28759 USA;[3]Northeast Forestry Univ, State Key Lab Tree Genet & Breeding, Harbin 150040, Peoples R China;[4]Natl Taiwan Univ, Dept Life Sci, Coll Life Sci, Taipei 10617, Taiwan;[5]Chinese Acad Forestry, State Key Lab Tree Genet & Breeding, Beijing 100091, Peoples R China;[6]Natl Chung Hsing Univ, Dept Forestry, Taichung 40227, Taiwan;[7]North Carolina State Univ, Dept Forest Biomat, Raleigh, NC 27695 USA

年份：2017

卷号：245

期号：5

起止页码：927-938

外文期刊名：PLANTA

收录：;WOS:【SCI-EXPANDED(收录号:WOS:000399445800005)】；

基金：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).

语种：英文

外文关键词：Wood formation; Transcriptome; Fiber cells; Vessel elements; Cell wall biosynthesis; Co-expression network

摘要：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.