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.

Figure 1

Recombination events and 7G8 allele frequency along each of the 14 P. falciparum chromosomes. Each panel represents one chromosome as marked (chr). Recombination events (black vertical lines) are the number of changes in inheritance pattern (parental allelic type) between two adjacent markers among 32 progeny, and 7G8 allele frequency is the proportion of 7G8 alleles among the 7G8 × GB4 progeny (red curves). The arrowheads under each panel indicate the positions of putative centromeres for the 14 chromosomes according to [11]. The dashed horizontal lines delimit the significant inheritance bias from 1:1 segregation.

Figure 2

Physical and genetic maps of the 14 P. falciparum chromosomes in the 7G8 × GB4 cross. The vertical red scale lines on the left indicate genetic distance in centimorgans, and the blue vertical lines on the right are the physical distance in kilobases. Thin grey lines connect the genetic position of each marker (3,184 mSFP and 254 microsatellite markers) with their mapped physical positions on the chromosome. Please see Additional file 3 for detailed information. Note the elevated recombination activities at chromosome ends, particularly those at ends of chromosomes 2, 3, 4, 8, and 9, which increase the estimate of genome-wide recombination rate. Maps after removing subtelomeric markers are shown in Additional file 10. The arrowheads on the right side of the blue vertical lines indicate the positions of putative centromeres for the 14 chromosomes according to [11].

Figure 3

Plot of recombination rate of the 7G8 × GB4 cross showing recombination hotspots along each of the 14 P. falciparum chromosomes. A region was considered a recombination hotspot (asterisks) if there were two or more recombination events across the 32 progeny and the estimated recombination rates were higher than the chromosome-wide average rate by five-fold or more. The 14 chromosomes are as marked and separated with the vertical dashed lines. The black asterisks are hotspots from the 7G8 × GB4 cross, and the red asterisks indicate hotspot positions from the Dd2 × HB3 cross. The arrowheads under each panel indicate the positions of putative centromeres for the 14 chromosomes according to [11].

Figure 4

Motifs enriched in recombination hotspot sequences. Motifs were identified from hotspot sequences using anr (any number of repetitions) in MEME. (a) A 21-bp motif from subtelomeric hotspot sequences of the 7G8 × GB4 cross that is similar to that of the Rep20 repeat reported previously [21-23]. (b) A GC-rich 12-bp repeat from subtelomeric hotspot sequences of the 7G8 × GB4 cross. (c) A 12-bp G/C-rich motif from the non-subtelomeric combined hotspot sequences of both crosses. (d,e) Two 12-bp G/C-rich motifs from subtelomeric and nonsubtelomeric sequences with at least one crossover within 5-kb interval, respectively, from the 7G8 × GB4 cross.