Chromosome-scale assembly with Hi-C data
Hi-C libraries were constructed from approximately 2 g of fresh leaves
following Miele et al . (2009), which included chromatin
extraction and digestion and DNA ligation, purification and
fragmentation. Then, these libraries were submitted for sequencing using
the Illumina HiSeq X Ten platform (Illumina, CA, USA). The generated
clean Hi-C data were mapped to the draft genome using BWA v. 0.7.1753
(Li & Durbin, 2009). The uniquely mapped Hi-C data were retained,
clustered, ordered and placed onto the 20 pseudochromosomes using
LACHESIS (Burton et al., 2013). A heat map of the interaction matrix of
all pseudochromosomes was plotted with a resolution of 100 kb.