Journal Article

Transcriptional landscape of sweetpotato root tip development at the single-cell level

Zhao, Nan, Liu, Hao, Ding, Xiawei, Huang, Lifei, Tian, CaiHuan, Xie, Shuyan, Wang, Shixin, lian Liang, Xue, Zou, Hongda, Chen, Jingyi

2024

Overview

Single-cell transcriptome sequencing (scRNA-seq) is a powerful tool for describing the transcriptome dynamics of plant development but has not yet been utilized to analyze the tissue ontology of sweetpotato. This study established a stable method for isolating single protoplast cells for scRNA-seq to reveal the cell heterogeneity of sweetpotato root tip meristems at the single-cell level. The study analyzed 12,172 single cells and 27,355 genes in the root tips of the sweetpotato variety Guangshu 87, which were distributed into 15 cell clusters. Pseudo-time analysis showed that there were transitional cells in the apical development trajectory of mature cell types from stem cell niches. Furthermore, we identified novel development regulators of sweetpotato tubers via trajectory analysis. The transcription factor IbGATA4 was highly expressed in the adventitious roots during the development of sweetpotato root tips, where it may regulate the development of sweetpotato root tips. In addition, significant differences were observed in the transcriptional profiles of cell types between sweetpotato, Arabidopsis thaliana , and maize. This study mapped the single-cell transcriptome of sweetpotato root tips, laying a foundation for studying the types, functions, differentiation, and development of sweetpotato root tip cells. Highlights This is the first single-cell transcriptional atlas of sweetpotato root apex tissue. Single-cell analysis of stem cell niche initiation showed unique transitional states. Sweetpotato, Arabidopsis , and maize root tip cell types were correlated. GATA4 may be involved in regulating sweetpotato root tip development.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Agriculture / Arabidopsis - genetics / Arabidopsis - growth & development / Arabidopsis thaliana / Biomedical and Life Sciences / Cell differentiation / Cluster analysis / Control / Corn / Developmental trajectory / Diseases and pests / Energy resources / Environmental aspects / Gene expression / Gene Expression Profiling / Gene Expression Regulation, Plant / Genetic aspects / Genomes / Genomics / Growth / Heterogeneity / Identification and classification / Ipomoea batatas / Ipomoea batatas (L.) Lam / Ipomoea batatas - genetics / Ipomoea batatas - growth & development / Ipomoea batatas - metabolism / Life Sciences / Meristem - genetics / Meristem - growth & development / Meristems / Metabolism / Metabolites / Plant breeding / Plant cells / plant development / Plant Proteins - genetics / Plant Proteins - metabolism / Plant Roots - genetics / Plant Roots - growth & development / Plant Sciences / protoplasts / Root / root tips / scRNA-seq / Single-Cell Analysis / Stem cells / Sweet potatoes / Tips / Trajectory analysis / transcription (genetics) / transcription factors / Transcription Factors - genetics / Transcription Factors - metabolism / Transcriptome / Transcriptomes / Transitional cells / Tree Biology / Zea mays - genetics / Zea mays - growth & development