Fig. 2

Single-cell RNA-seq and cluster annotation of cotton hypocotyl. a Overview of cotton hypocotyl scRNA-seq workflow. Protoplasts were isolated from hypocotyl sections of Jin668 and TM-1 with two independent biological repeats, respectively. 10 × Genomics platform was used for high-throughput sequencing. b, c UMAP visualization shows these cotton hypocotyl cells were grouped in to 9 clusters both in Jin668 and TM-1. Each dot indicates a single cell. Different colors indicate cell clusters. d Marker genes of each cell cluster in Jin668 and TM-1. e RNA in situ hybridization of 3 selected genes, including Ghir_A01G019320 in primary xylem (PX), Ghir_D11G036340 in xylem vessel precursors (XV), and Ghir_A10G018730 in phloem (indicated by red arrow). Scale bar, 50 μm