Transcriptional landscape of highly lignified poplar stems at single-cell resolution

Abstract

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.

Single‐cell transcriptome atlas reveals developmental trajectories and a novel metabolic pathway of catechin esters in tea leaves

“…Based on the specific unique molecular identification of single‐cell, scRNA‐seq enable monitoring of intracellular transcriptional activity at the single‐cell level (Seyfferth et al ., 2021 ). Currently, scRNA‐seq of several plant species, such as Arabidopsis, strawberry, rice and maize, peanuts, and one woody plant populus were reported (Bai et al ., 2022 ; Chen et al ., 2021 ; Kim et al ., 2021 ; Li et al ., 2021 ; Liu et al ., 2020 , 2021 ; Marand et al ., 2021 ; Xie et al ., 2021 ; Zhang et al ., 2021a , b ). Through these studies, a database of cell‐specific markers and a single‐cell atlas of various tissues and organs from different species has been established, providing new insights into organ development, cell differentiation and cell division (Jin et al ., 2021 ).…”

“…Leaf is one of the principal vegetative organs of vascular plants for photosynthesis and transpiration. Until now, only a stem cell atlas of populus has been reported for woody plants; scRNA‐seq applications of woody leaves are not yet available (Chen et al ., 2021 ; Li et al ., 2021 ; Xie et al ., 2021 ). Compared with the leaf structure of herbaceous plants, tea leaves have a well‐developed secondary cell wall, strong vascular bundles and a thick wax layer etc.…”

“…been reported for woody plants; scRNA-seq applications of woody leaves are not yet available (Chen et al, 2021;Xie et al, 2021). Compared with the leaf structure of herbaceous plants, tea leaves have a well-developed secondary cell wall, strong vascular bundles and a thick wax layer etc.…”

Current Understanding of the Genetics and Molecular Mechanisms Regulating Wood Formation in Plants

“…The contribution of various cell types to wood formation is not well understood; until now, only tissue-level analysis was possible. Very recently, single-cell RNA-seq enabled the analysis of the wood formation control network at the single-cell level [ 108 , 109 ]. In the future, new information on the molecular mechanisms involved in wood formation will likely be obtained through studies using the latest technologies, which are rapidly being developed and applied.…”

Single‐cell RNA‐seq reveals fate determination control of an individual fibre cell initiation in cotton (Gossypium hirsutum)

“…Subsequently, a series of developmental processes in Arabidopsis had been explored at single cell resolution, such as the development of root tips (Denyer et al ., 2019 ; Jean‐Baptiste et al ., 2019 ; Shahan et al ., 2022 ; Wendrich et al ., 2020 ; Zhang et al ., 2019 ), lateral root (Gala et al ., 2021 ), vegetative shoot apex (Zhang et al ., 2021b ), stomatal cell lineage (Liu et al ., 2020 ), developing leaf (Kim et al ., 2021 ; Liu et al ., 2022a ; Lopez‐Anido et al ., 2021 ; Tenorio Berrio et al ., 2022 ) and vein pattern in the cotyledons (Liu et al ., 2022b ). At the same time, scRNA‐seq has also been widely used in other plants, including rice (Liu et al ., 2021b ; Wang et al ., 2021b ; Zhang et al ., 2021a ; Zong et al ., 2022 ), corn (Li et al ., 2022 ; Ortiz‐Ramirez et al ., 2021 ; Satterlee et al ., 2020 ; Sun et al ., 2022 ; Xu et al ., 2021 ), peanut (Liu et al ., 2021a ), tea plant (Wang et al ., 2022 ), tomato (Omary et al ., 2022 ) and poplar (Chen et al ., 2021 ; Li et al ., 2021 ; Xie et al ., 2022 ). These studies provide new insights into heterogeneity of gene expression between different cell types, and molecular trajectory of cell differentiation during development.…”