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.