Single-cell transcriptome reveals the redifferentiation trajectories of the early stage of de novo shoot regeneration in Arabidopsis thaliana

Abstract

De novo shoot regeneration from a callus plays a crucial role in both plant biotechnology and the fundamental research of plant cell totipotency. Recent studies have revealed many regulatory factors involved in this developmental process. However. our knowledge of the cell heterogeneity and cell fate transition during de novo shoot regeneration is still limited. Here, we performed time-series single-cell transcriptome experiments to reveal the cell heterogeneity and redifferentiation trajectories during the early stage of de novo shoot regeneration. Based on the single-cell transcriptome data of 35,669 cells at five-time points, we successfully determined seven major cell populations in this developmental process and reconstructed the redifferentiation trajectories. We found that all cell populations resembled root identities and undergone gradual cell-fate transitions. In detail, the totipotent callus cells differentiated into pluripotent QC-like cells and then gradually developed into less differentiated cells that have multiple root-like cell identities, such as pericycle-like cells. According to the reconstructed redifferentiation trajectories, we discovered that the canonical regeneration-related genes were dynamically expressed at certain stages of the redifferentiation process. Moreover, we also explored potential transcription factors and regulatory networks that might be involved in this process. The transcription factors detected at the initial stage, QC-like cells, and the end stage provided a valuable resource for future functional verifications. Overall, this dataset offers a unique glimpse into the early stages of de novo shoot regeneration, providing a foundation for a comprehensive analysis of the mechanism of de novo shoot regeneration.

Unleashing the power within short-read RNA-seq for plant research: Beyond differential expression analysis and toward regulomics

“…More recently, short-read RNA-seq has been pushed to single-cell resolution due to a series of technological advancements, including robotics, microfluidics and hydrogel droplets ( Zhang et al., 2019 ). In a few years, efforts in single-cell RNA-seq (scRNA-seq) or single-nuclei RNA-seq (snRNA-seq) have expanded from model plants (Arabidopsis, tomato and rice) to non-model species (e.g., maize and poplar), from organ development and cell differentiation to wood formation ( Gutzat et al., 2020 ; Xu et al., 2020 ; Li et al., 2021 ; Kajala et al., 2021 ; Chen et al., 2021a ; Wang et al., 2021 ; Bezrutczyk et al., 2021 ; Liu et al., 2022 ). Undoubtedly, single-cell transcriptomics are leading the fore frontier of plant single-cell biology and playing an ever-increasing role in plant research and breeding.…”