title: High recombination rates and hotspots in a Plasmodium falciparum genetic cross.
abstract: BACKGROUND
  The human malaria parasite Plasmodium falciparum survives pressures from the host immune system and antimalarial drugs by modifying its genome. Genetic recombination and nucleotide substitution are the two major mechanisms that the parasite employs to generate genome diversity. A better understanding of these mechanisms may provide important information for studying parasite evolution, immune evasion and drug resistance.
  
  
  RESULTS
  Here, we used a high-density tiling array to estimate the genetic recombination rate among 32 progeny of a P. falciparum genetic cross (7G8 × GB4). We detected 638 recombination events and constructed a high-resolution genetic map. Comparing genetic and physical maps, we obtained an overall recombination rate of 9.6 kb per centimorgan and identified 54 candidate recombination hotspots. Similar to centromeres in other organisms, the sequences of P. falciparum centromeres are found in chromosome regions largely devoid of recombination activity. Motifs enriched in hotspots were also identified, including a 12-bp G/C-rich motif with 3-bp periodicity that may interact with a protein containing 11 predicted zinc finger arrays.
  
  
  CONCLUSIONS
  These results show that the P. falciparum genome has a high recombination rate, although it also follows the overall rule of meiosis in eukaryotes with an average of approximately one crossover per chromosome per meiosis. GC-rich repetitive motifs identified in the hotspot sequences may play a role in the high recombination rate observed. The lack of recombination activity in centromeric regions is consistent with the observations of reduced recombination near the centromeres of other organisms.
authors.affiliation: Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA.
authors.forename: Hongying
authors.initials: H
authors.lastname: Jiang
authors.forename: Na
authors.initials: N
authors.lastname: Li
authors.forename: Vivek
authors.initials: V
authors.lastname: Gopalan
authors.forename: Martine M
authors.initials: MM
authors.lastname: Zilversmit
authors.forename: Sudhir
authors.initials: S
authors.lastname: Varma
authors.forename: Vijayaraj
authors.initials: V
authors.lastname: Nagarajan
authors.forename: Jian
authors.initials: J
authors.lastname: Li
authors.forename: Jianbing
authors.initials: J
authors.lastname: Mu
authors.forename: Karen
authors.initials: K
authors.lastname: Hayton
authors.forename: Bruce
authors.initials: B
authors.lastname: Henschen
authors.forename: Ming
authors.initials: M
authors.lastname: Yi
authors.forename: Robert
authors.initials: R
authors.lastname: Stephens
authors.forename: Gilean
authors.initials: G
authors.lastname: McVean
authors.forename: Philip
authors.initials: P
authors.lastname: Awadalla
authors.forename: Thomas E
authors.initials: TE
authors.lastname: Wellems
authors.forename: Xin-zhuan
authors.initials: XZ
authors.lastname: Su
mesh_terms: D002874:Chromosome Mapping; D003433:Crosses, Genetic; D003434:Crossing Over, Genetic; D014644:Genetic Variation; D018503:Genome, Protozoan; D006801:Humans; D008288:Malaria / Q000469:parasitology; D008540:Meiosis / Q000235:genetics*; D010963:Plasmodium falciparum / Q000235:genetics*; D011995:Recombination, Genetic / Q000235:genetics*