Fig. 2

Phylogeny and variation landscapes from 18 B. rapa representative genomes and 524 resequenced accession genomes. a Phylogenetic relationships of 18 B. rapa accessions using B. oleracea as an outgroup. The branch length values represent divergence between accessions with B. oleracea. b A neighbor-joining tree of 524 B. rapa accessions. Different colors indicate the accessions within different sub-populations, and the 18 B. rapa genomes are specifically marked with red stars. Representative morphological pictures are displayed next to the corresponding sub-populations. c Distribution of genomic variants from 18 genomes and 524 accessions on 10 B. rapa chromosomes using Chiifu as the reference. d Correlation between SNP densities detected by resequencing data of the B. rapa germplasm (x-axis) and comparison of de novo assemblies (y-axis). We calculated the number of SNPs in a bin with a size of 500 kb. e SV number plots against repetitive sequences. We used deletion sequences to evaluate the correlation between SV and repetitive sequences involvement. Red (blue) indicates that the proportion of repetitive sequences in the SV sequence is less (greater) than 80%. f The number of SVs after different combinations of individuals. g An ~1.3 Mb inversion specifically occurred in the Chiifu and CCB genomes