Genomic sequencing reads from Plasmodium knowlesi strain H substrain YH1
Plasmodium knowlesi H substrain YH1 was cloned and amplified in human blood that had been depleted of white blood cells (Interstate Blood Bank Inc). DNA was prepared using the Qiagen DNeasy blood and tissue kit following the manufacturer's instructions. Library construction and sequencing were preformed at the Broad Institute, Cambridge, MA, USA. Illumina fragment libraries were generated as previously described (PMID: 18987734) with the following modifications. For each sample, 100 ng of genomic DNA was sheared to 200 bp in size using a Covaris LE220 instrument (Covaris, MA) with the following parameters: temperature: 7–9 °C; duty cycle: 20%; intensity: 5; cycles per burst: 200; time: 90 s; shearing tubes: Crimp Cap microTUBES with AFA fibers Covaris, MA). DNA fragments were end repaired, 3’ adenylated, ligated with indexed Illumina sequencing adapter, and PCR enriched, as previously described (PMID: 21205303). The resulting Illumina fragment sequencing libraries were normalized and were size selected to contain inserts of 180 bp ± 3% in length using a Pippen Prep system (Sage Science, MA) following the manufacturer’s recommendations. Illumina sequencing libraries were quantified using quantitative PCR (KAPA Biosystems, MA) following the manufacturer’s recommendations. Libraries were normalized to 2 nM and denatured using 0.1 N NaOH. Sequencing Flowcell cluster amplification was performed according to the manufacturer’s recommendations using the V3 TruSeq PE Cluster Kit and V3 TruSeq Flowcells (Illumina, CA). Flowcells were sequenced with 101 base paired end reads on a Illumina HiSeq2500 instrument, using V3 TruSeq Sequencing by synthesis kits and analyzed with the Illumina RTA v1.12 pipeline (Illumina, CA).