Whole genome Illumina sequencing of Plasmodium knowlesi Malayan Strain Pk1 (A+)
Synchronized, P. knowlesi blood-stage trophozoites were crosslinked. Nuclei were isolated after homogenization. In situ Hi-C protocol was performed.  Briefly, nuclei were permeabilized, DNA was digested with Mbol, the ends of restriction fragments were filled with biotinylated nucleotides and ligated using T4 DNA ligase. After reversal of crosslinks, ligated DNA was purified and size-selected.  Ligated fragments were pulled down using streptavidin beads and prepped for Illumina sequencing by subsequent end-repair, addition of A-overhangs and adapter ligation. Libraries were PCR-amplified and sequenced with a NextSeq500 DNA sequencer, generating 75 bp paired-end sequence reads.