Hi-C library preparation and data analysis
In the present study, 8 g of young leaf tissue collected from the sameB. rapa var. parachinensis plant was used for Hi-C library construction. The Hi-C experiment consisted of the following steps: crosslinking, lysis, chromatin digestion, biotin marking, proximity ligations, cross linking reversal, and DNA purification(Xuefen Yang et al., 2019). The purified and enriched DNA was used for the sequencing library construction; the DNA was sequenced using the Illumina HiSeq 2000 platform (Illumina, USA). The overlapping group was hitched to the scaffold level using Juicer(Durand et al., 2016) and 3D-DNA(Dudchenko et al., 2017). MCScanX(Y. Wang et al., 2012) was used to make a collinear comparison between scaffolds and the existing B. rapagenome(Cai et al., 2017). The sequence was given a new name after being manually assembled to the chromosome.
We used bwa mem(Vasimuddin, Misra, Li, & Aluru, 2019) to map two paired reads to the chromosome level genome sequence alone with these parameters “-A1 -B4 -E50 -L0”. Then HiCExplorer kit(Wolff et al., 2018) was used to build a Hi-C contact map. Parameters for the step hicCorrectMatrix were set to “–filterThreshold -3.5 5” and the rests were kept at default settings.