PMID- 34809675 OWN - NLM STAT- MEDLINE VI - 22 IP - 1 TI - Transcriptional landscape of highly lignified poplar stems at single-cell resolution. PG - 319 CI - © 2021. The Author(s). LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Genome Biol JT - Genome biology JID - 100960660 IS - 1474-760X (Electronic) LID - 10.1186/s13059-021-02537-2 [doi] FAU - Chen, Yang AU - Chen Y AD - Key Laboratory of Bio-resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China. FAU - Tong, Shaofei AU - Tong S AD - Key Laboratory of Bio-resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China. FAU - Jiang, Yuanzhong AU - Jiang Y AD - Key Laboratory of Bio-resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China. FAU - Ai, Fandi AU - Ai F AD - Key Laboratory of Bio-resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China. FAU - Feng, Yanlin AU - Feng Y AD - Key Laboratory of Bio-resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China. FAU - Zhang, Junlin AU - Zhang J AD - Key Laboratory of Bio-resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China. FAU - Gong, Jue AU - Gong J AD - Key Laboratory of Bio-resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China. FAU - Qin, Jiajia AU - Qin J AD - Key Laboratory of Bio-resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China. FAU - Zhang, Yuanyuan AU - Zhang Y AD - Key Laboratory of Bio-resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China. FAU - Zhu, Yingying AU - Zhu Y AD - State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, Lanzhou, China. FAU - Liu, Jianquan AU - Liu J AD - Key Laboratory of Bio-resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China. AD - State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, Lanzhou, China. FAU - Ma, Tao AU - Ma T AUID- ORCID: 0000-0002-7094-6868 AD - Key Laboratory of Bio-resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China. matao.yz@gmail.com. IS - 1474-7596 (Linking) RN - 0 (Genetic Markers) RN - 0 (Plant Growth Regulators) RN - 0 (Plant Proteins) SB - IM MH - Biomass MH - Cambium/genetics/growth & development/metabolism MH - *Gene Expression Regulation, Plant MH - Genetic Markers MH - Multigene Family MH - Phloem/growth & development/metabolism MH - Plant Growth Regulators/metabolism MH - Plant Proteins/genetics MH - Plant Stems/*genetics/*metabolism MH - Populus/*genetics/*metabolism MH - RNA-Seq MH - Single-Cell Analysis MH - Transcriptome MH - Trees MH - Xylem/growth & development/metabolism PMC - PMC8607660 DCOM- 20220315 LR - 20231108 DP - 20211122 DEP - 20211122 AB - BACKGROUND: Plant secondary growth depends on the activity of the vascular cambium, which produces xylem and phloem. Wood derived from xylem is the most abundant form of biomass globally and has played key socio-economic and subsistence roles throughout human history. However, despite intensive study of vascular development, the full diversity of cell types and the gene networks engaged are still poorly understood. RESULTS: Here, we have applied an optimized protoplast isolation protocol and RNA sequencing to characterize the high-resolution single-cell transcriptional landscape of highly lignified poplar stems. We identify 20 putative cell clusters with a series of novel cluster-specific marker genes and find that these cells are highly heterogeneous based on the transcriptome. Analysis of these marker genes' expression dynamics enables reconstruction of the cell differentiation trajectories involved in phloem and xylem development. We find that different cell clusters exhibit distinct patterns of phytohormone responses and emphasize the use of our data to predict potential gene redundancy and identify candidate genes related to vascular development in trees. CONCLUSIONS: These findings establish the transcriptional landscape of major cell types of poplar stems at single-cell resolution and provide a valuable resource for investigating basic principles of vascular cell specification and differentiation in trees.