RT Journal Article SR Electronic T1 Genome variation and meiotic recombination in Plasmodium falciparum: insights from deep sequencing of genetic crosses JF bioRxiv FD Cold Spring Harbor Laboratory SP 024182 DO 10.1101/024182 A1 Alistair Miles A1 Zamin Iqbal A1 Paul Vauterin A1 Richard Pearson A1 Susana Campino A1 Michel Theron A1 Kelda Gould A1 Daniel Mead A1 Eleanor Drury A1 John O’Brien A1 Valentin Ruano Rubio A1 Bronwyn Macinnis A1 Jonathan Mwangi A1 Upeka Samarakoon A1 Lisa Ranford-Cartwright A1 Michael Ferdig A1 Karen Hayton A1 Xinzhuan Su A1 Thomas Wellems A1 Julian Rayner A1 Gil McVean A1 Dominic Kwiatkowski YR 2015 UL http://biorxiv.org/content/early/2015/08/07/024182.abstract AB The malaria parasite Plasmodium falciparum has a great capacity for evolutionary adaptation to evade host immunity and develop drug resistance. Current understanding of parasite evolution is impeded by the fact that a large fraction of the genome is either highly repetitive or highly variable, and thus difficult to analyse using short read technologies. Here we describe a resource of deep sequencing data on parents and progeny from genetic crosses, which has enabled us to perform the first integrated analysis of SNP, INDEL and complex polymorphisms, using Mendelian error rates as an indicator of genotypic accuracy. These data reveal that INDELs are exceptionally abundant and the dominant mode of polymorphism within the core genome. We analyse patterns of meiotic recombination, including the relative contribution of crossover and non-crossover events, and we observe several instances of recombination that modify copy number variants associated with drug resistance. We describe a novel web application that allows these data to be explored in detail.