Genome assemblies of 12 rice inbred lines.

Draft genomes of the 12 rice inbred lines were assembled using HiFi reads with parameter -l3 via HiFiasm (v0.19.5). De novo genome assemblies of two representative ILs, YB and Balilla, were performed with the aid of Hi-C data, yielding an average sequencing depth at 127.80×. The clean Hi-C reads for YB and Balilla were aligned to contigs using Juicer (v1.6). Contact matrices were generated with 3D-DNA (v180922, -r0), and corrections were applied using JuiceBox (v1.11.08). The genomes at the chromosome level of the remained 10 ILs were assembled based on one of these two reference genomes using Ragtag (v2.1.0, scaffold). We assessed the accuracy, identity, and completeness of the 12 assemblies. The completeness of the assemblies was assessed using Benchmarking Universal Single-Copy Orthologue (v3.0.2, embryophyta_odb10) analysis. The long terminal repeats (LTR) assembly index (LAI) was calculated for each chromosome using LTR tools, including LTR_retriever (v2.9.0, -infinder ltrfinder.scn -inharvest ltrharvest.scn), LTR_FINDER (v1.0.7, -D 15000 -L 7000 -C -M 0.7), and GenomeTools (v1.6.2, ltrharvest -similar 70 -vic 10 -seed 20 -seqids yes -maxlenltr 7000 -maxtsd 6). HiFi reads were re-mapped to the assemblies with parameters “-ax map-hifi” using Minimap2 (v2.21).