analysis Surrounding HRP2 3 deletions

Welcome to the analysis of the regions surrounding HRP2 and HRP3 genomic deletions

Website Outline

This is an outline of the website what each subsection contains

• Window Analysis
  • This subsection contains information on the windows selected for analysis on chromosomes 8, 11 and 13. This includes the genomic locations of the windows as well as the coverage and diversity of the windows.
    
• Additional Genotyping
  • Genotyping on parasites outside of the chr 8, 11, 13 regions studied here this includes:
    • Drug resistance
    • Microhaplotypes
• HB3/SD01 Longreads analysis
  • This subsection has all the code used to analyze both the old Pacbio(Otto, Böhme, et al. 2018) long reads and novel nanopore long reads
  • This includes the assembly of the HB3/SD01 strains using Oxford nanopore and the comparison to the previous assemblies of these strains and to 3D7
    
• Related Genomic Regions Vis
  • This focuses on the related regions to HRP2 and HRP3 and their deletions
  • This includes visualization on shared segements between 3D7 chromosomes
  • This also includes some miscellaneous information on variation important regions including rRNA (involved in the deletion and subsequent duplication of chr11)
    
• Comparing to related Plasmodiums
  • Comparing the falciparum hrp2/hrp3 proteins to the other closely related plasmodiums in the Laverenia genus(Otto, Gilabert, et al. 2018)
• References
  • Contains the bibliography mentioned in the website on the tools and previous publications
    
  • Also has the R version and the packages used for data analysis

Major Points from analysis:

• HRP3 genomic deletion occurs in 2 patterns
  • Pattern 1 involves a concurrent duplication event of chr11 from a 15.2kb homologous region shared between 11 and 13
    
  • Pattern 2 a break centromeric to HPR3 but before the the homologous region which does not include a duplication event
    
• Deletion geographical distribution
  • Pattern 1deletion almost exclusively only seen in Africa and South America while pattern 2 deletion almost exclusive seen in South East Asia
    
• Proof of pattern 1
  • Paper in 1994 (Hinterberg et al. 1994) showed Chr 13 Deletion and chr 11 duplication event already discussed in HB3 which has known HRP3 deletion but seen by examining restriction site presence of DNA probes
    
  • Our work utilizes long reads of nanopore to prove spanning raw reads across a hybrid chr11-13 as well as assembled contigs that span this region as well for HB3 as well as a new clinical strain SD01 from the South Sudan region
• Pattern 1 diversity
  • Chr 11 duplicated region
    
  • Majority of clones have a perfect copy of chr 11 segment
    
  • Those with divergent copies can be quite divergent averaging 89% conserved between copies
    
  • This duplicated region haplotypes are also circulating through out the general population in parasites without duplication
    • None of them can be found within the South East Asia population
• Pattern 1 breakpoint
  • The fact that parasites with perfect chr 11 segment duplications have variations with the homologous region would suggest that the breakpoint that leads to the deletion duplication event lies directly within this region.
    
• The converse to pattern 1 is not observed
  • Parasites with chr 11 deleted and chr 13 are not observed
    
  • E.g. where parasites lack chromosome 11 from the homologous region onwards replaced by chr 13 from it’s homologous region
    
  • Unknown is why this is and there could be several reasons why
    • mechanistically impossible
      • As it’s unknown where and when these deletions are occurring along the parasites life cycle (mitosis vs meiosis vs both) is somehow not possible for the chr13 to transpose onto chr 11
        
      • This seems unlikely as if chr 11 can transpose onto chr13 there’s nothing obvious that would suggest that the reverse should be impossible. As clone FCR3’s genomic coverage argues that it’s possible as it appears to have two chr 13 and no chr 11
        
    • selective pressure
      • This pressure could be in a couple of ways
        • the absence of this chromosome 11 segment is so detrimental to parasite survival that no parasites missing this portion can even survive
          
        • the presence of two copies of this chromosome 13 segment is so detrimental to parasite survival that no parasites with two copies can survive
          
        • the presence of 1 or more copies of chromosome 11 gives so much greater advantage over it’s absence that any parasites lacking chromosome 11 segment get out competed by parasites containing this chromosome to such a degree that no chromosome 13 duplicated parasite circulate in the population
          
  • The fact that there are circulating pattern 1 parasites without the presence of even 1 parasite with the reverse pattern even in regions like South America where RDTs are not used the pressure or mechanism behind the absence of the reverse of pattern 1 must be extreme and is not being driven by RDT usage

References

Hinterberg, K, D Mattei, T E Wellems, and A Scherf. 1994. “Interchromosomal Exchange of a Large Subtelomeric Segment in a Plasmodium Falciparum Cross.” EMBO J. 13 (17): 4174–80.

Otto, Thomas D, Ulrike Böhme, Mandy Sanders, Adam Reid, Ellen I Bruske, Craig W Duffy, Pete C Bull, et al. 2018. “Long Read Assemblies of Geographically Dispersed Plasmodium Falciparum Isolates Reveal Highly Structured Subtelomeres.” Wellcome Open Res 3 (May): 52.

Otto, Thomas D, Aude Gilabert, Thomas Crellen, Ulrike Böhme, Céline Arnathau, Mandy Sanders, Samuel O Oyola, et al. 2018. “Genomes of All Known Members of a Plasmodium Subgenus Reveal Paths to Virulent Human Malaria.” Nat Microbiol 3 (6): 687–97.