Fig. 1: Genomic features and population structure of 165 rice accessions.

a Circos plot illustrating the genomic characteristics of the TB accession. The outer to inner circles represent: chromosomes (with centromeres highlighted in dark blue), gene density, Gypsy density, Helitron density, GC content, structural variation (SV) density, and TIP density. The shades transitioning from light to dark indicate increasing numerical values. The numbers labeling the outer circle indicate the length (Mb) of each chromosome. b TE content across the 10 rice assemblies. The phylogenetic tree was constructed based on single-copy genes from the assemblies. c Variation in gene families within the pan-genome and core genome as the number of rice genomes increases. d The number of different TE insertions in genic regions, which include sequences 2 kb upstream and downstream of each gene body. e Principal component analysis (PCA) plot of 165 rice accessions based on TIPs. f Population structure analysis conducted for 165 accessions with varying ancestry kinship (K  =  2–7) based on TIPs. Each vertical bar represents an accession, and the x-axis displays the different subpopulations¹⁴⁵: Aus (aus), Ind I (indica I), Ind II (indica II), Ind III (indica III), Ind int (indica intermediate), Int (intermediate), Jap int (japonica intermediate), Tem jap (temperate japonica) and Tro jap (tropical japonica). The y-axis quantifies ancestry membership. Source data are provided as a Source Data file.