Structural variants analysis
Structural variations were detected using an assembly-based pipeline based on LASTZ/CHAIN/NET/NETSYNTENY tools(Harris, 2007; Kent, Baertsch, Hinrichs, Miller, & Haussler, 2003; Liao, Zhang, Chakraborty, & Emerson, 2020; Schwartz et al., 2003) which is publicly available at https://github.com/yiliao1022/LASTZ_SV_pipeline. Insertion times of LTR-retrotransposons were estimated by the divergence time (T) between the two LTRs of each intact element with the formula: T= K/2r, where Ks refers to the sequence difference between the 5’-LTR and 3’-LTR of an intact LTR element and r refers to the average mutation rate. Here we used the neutral substitution rate of 1.5X 10-8 per synonymous site per generation(Koch, Haubold, & Mitchell-Olds, 2000).

Figure 1. Overview of the assembly pipeline for Brassica rapa var. parachinensis genome. The steps include assembly of PacBio reads followed by scaffolding using Hi-C, and extensive QC using high coverage of Illumina short reads followed by de novo repeat annotation and gene annotation using ISO-seq sequencing.