DNA sequence analysis

A total of 343 rice accessions were re-sequenced using the Illumina NovaSeq6000 platform, and sequencing data analysis was performed using the pipeline from our previous study (Wang et al. 2023; Yang et al. 2023). Firstly, the adaptor sequences and low-quality sequence reads were removed from the data sets, and raw sequences were transformed into clean reads after data processing. Next, the clean reads were mapped to the reference genome sequence and only reads with a perfect match or one mismatch were further analyzed and annotated based on the Nipponbare IRGSP1.0 genome using Hisat2 tools soft. Finally, GATK software was used to detect SNP and Indel (≦ 50 bp) and PAVs (the presence/absence variation > 50 bp) were called based on the mapping coverage of sequencing reads to the pangenome for each accession. All raw sequence data have been deposited in the NCBI sequence read archive (BioProject accession PRJNA820969).