Rapid whole genome optical mapping of Plasmodium falciparum

Background: Immune evasion and drug resistance in malaria have been linked to chromosomal recombination and gene copy number variation (CNV). These events are ideally studied using comparative genomic analyses; however in malaria these analyses are not as common or thorough as in other infectious diseases, partly due to the difficulty in sequencing and assembling complete genome drafts. Recently, whole genome optical mapping has gained wide use in support of genomic sequence assembly and comparison. Here, a rapid technique for producing whole genome optical maps of Plasmodium falciparum is described and the results of mapping four genomes are presented. Methods: Four laboratory strains of P. falciparum were analysed using the Argus (TM) optical mapping system to produce ordered restriction fragment maps of all 14 chromosomes in each genome. Plasmodium falciparum DNA was isolated directly from blood culture, visualized using the Argus (TM) system and assembled in a manner analogous to next generation sequence assembly into maps (AssemblyViewer (TM), OpGen Inc.(R)). Full coverage maps were generated for P. falciparum strains 3D7, FVO, D6 and C235. A reference P. falciparum in silico map was created by the digestion of the genomic sequence of P. falciparum with the restriction enzyme AflII, for comparisons to genomic optical maps. Maps were then compared using the MapSolver (TM) software. Results: Genomic variation was observed among the mapped strains, as well as between the map of the reference strain and the map derived from the putative sequence of that same strain. Duplications, deletions, insertions, inversions and misassemblies of sizes ranging from 3,500 base pairs up to 78,000 base pairs were observed. Many genomic events occurred in areas of known repetitive sequence or high copy number genes, including var gene clusters and rifin complexes. Conclusions: This technique for optical mapping of multiple malaria genomes allows for whole genome comparison of multiple strains and can assist in identifying genetic variation and sequence contig assembly. New protocols and technology allowed us to produce high quality contigs spanning four P. falciparum genomes in six weeks for less than $1,000.00 per genome. This relatively low cost and quick turnaround makes the technique valuable compared to other genomic sequencing technologies for studying genetic variation in malaria.