TY  - JOUR
A1  - Miles, Alistair
A1  - Iqbal, Zamin
A1  - Vauterin, Paul
A1  - Pearson, Richard
A1  - Campino, Susana
A1  - Theron, Michel
A1  - Gould, Kelda
A1  - Mead, Daniel
A1  - Drury, Eleanor
A1  - O'Brien, John
A1  - Ruano Rubio, Valentin
A1  - MacInnis, Bronwyn
A1  - Mwangi, Jonathan
A1  - Samarakoon, Upeka
A1  - Ranford-Cartwright, Lisa
A1  - Ferdig, Michael
A1  - Hayton, Karen
A1  - Su, Xin-zhuan
A1  - Wellems, Thomas
A1  - Rayner, Julian
A1  - McVean, Gil
A1  - Kwiatkowski, Dominic
T1  - Indels, structural variation, and recombination drive genomic diversity in Plasmodium falciparum
Y1  - 2016/09/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 1288 
EP  - 1299 
DO  - 10.1101/gr.203711.115 
VL  - 26 
IS  - 9 
UR  - http://genome.cshlp.org/content/26/9/1288.abstract 
N2  - 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 analyze using short-read sequencing 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 genome-wide, 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, being more common than SNPs and thus the dominant mode of polymorphism within the core genome. We use the high density of SNP and indel markers to analyze patterns of meiotic recombination, confirming a high rate of crossover events and providing the first estimates for the rate of non-crossover events and the length of conversion tracts. We observe several instances of meiotic recombination within copy number variants associated with drug resistance, demonstrating a mechanism whereby fitness costs associated with resistance mutations could be compensated and greater phenotypic plasticity could be acquired. 
ER  -