Approximately 100 root tips were collected from S. kraussiana individuals cultured in soil and used for single-cell sequencing. The single-cell suspensions were loaded on a Chromium Single Cell Instrument following the manufacturer’s instructions for the 10× Genomics Chromium Single-Cell 3′ kit (v3). The libraries were sequenced on the Illumina NovaSeq 6000 platform by LC-Bio Technology (HangZhou, China). A total of 3969 single cells were used for further analyses.