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.