Single-cell transcriptomic analysis of rice root tips [scRNA-seq]

There are two main types of root systems in flowering plants, which are taproot systems in dicot and fibrous root systems in monocot. The cellular and molecular mechanism involved in root development are mainly from the study of dicot model Arabidopsis thaliana. However, mechanisms of root development and their conservation and divergence in monocot, which including the major crops, remain largely elusive. Here we profile the transcriptomes of more than 20,000 single cells in the root tips of two rice cultivars, Nipponbare (Nip; Japonica) and 93-11 (Indica). Single-cell analysis coupled with in situ hybridization identify the cell type-specific marker genes and annotate all the clusters. Comparison of single-cell transcriptome and analysis of mark gene expression suggest well-conserved molecular landscape between rice Nip and 93-11. Moreover, our analysis suggests specific functions gene expression patterns for each cell type cluster, including the hormone genes. Comparison to Arabidopsis single-cell RNA-sequencing dataset reveals extensive differences between Arabidopsis and rice cell types, and species-specific features emphasize the importance of directly studying rice root. Our study reveals transcriptome landscape of major cell types of rice root in singe-cell resolution and provides molecular insight of the cell type morphology of cell type evolution in plants. Overall design: Single-cell RNAseq of rice root tips

被子植物主要存在两类根系：双子叶植物的直根系（taproot system）与单子叶植物的须根系（fibrous root system）。根系发育所涉及的细胞与分子机制，主要源自对双子叶模式植物拟南芥（Arabidopsis thaliana）的研究。然而，作为主要粮食作物来源的单子叶植物，其根系发育机制以及这些机制的保守性与分化性，目前尚未阐明。本研究对两个水稻栽培品种——粳稻品种日本晴（Nipponbare，简称Nip）和籼稻品种93-11——的根尖组织，完成了逾20000个单细胞的转录组图谱构建。结合单细胞分析与原位杂交（in situ hybridization）技术，本研究鉴定了细胞类型特异性标记基因，并对所有细胞簇完成注释。通过对两个水稻品种的单细胞转录组进行比较并分析标记基因的表达模式，结果显示日本晴与93-11之间存在高度保守的分子调控图谱。此外，本研究分析表明，各细胞类型簇均具有独特的功能基因表达模式，其中涵盖激素相关基因。将本研究数据与拟南芥单细胞RNA测序（single-cell RNA-sequencing）数据集进行比较后发现，拟南芥与水稻的细胞类型间存在广泛差异，物种特异性特征凸显了直接开展水稻根系研究的重要性。本研究以单细胞分辨率揭示了水稻根系主要细胞类型的转录组图谱，并为阐释植物细胞类型形态及细胞类型演化提供了分子层面的见解。实验整体设计：水稻根尖单细胞RNA测序