Project Info

Project Information

We are sequencing two clones of Plasmodium falciparum that are instrumental in studies of malarial genetics, HB3 and Dd2, to better understand polymorphism in P. falciparum. These two clones are the parents of a widely used genetic cross and differ in the frequency of acquisition of drug resistance. The goal of the current project is to release an annotated assembly with ≥ 8X genome sequence coverage for Plasmodium falciparum clone HB3.

Collaborators for this project include: Dyann Wirth and Sarah Volkman, Harvard School of Public Health and Daniel Hartl, Harvard University.

Why are we sequencing different clones of P. falciparum?

Malaria is a major cause of morbidity and mortality worldwide, with an estimated 500 million new cases each year. Global incidence of this emerging infectious disease is increasing due to rising drug resistance and globalization. In 2002, malaria caused nearly half as many deaths as did AIDS, with most of these deaths being due to P. falciparum. Molecular approaches have helped identify many P. falciparum genes that are involved in drug resistance and parasite biology, and the availability of the genome sequence from a P. falciparum isolate grown in laboratory culture provides the foundation for systematic study of the biology of the parasite. In addition, genome resources are available for other Plasmodium species, including the genome sequence for P. vivax. However, recent evolutionary analysis indicates that the divergence between P. falciparum and these other parasites is so great that we must increase efforts to understand P. falciparum-specific biology.

Polymorphism in P. falciparum is known to be concentrated in genes that are involved in immune system evasion and pathogenicity. Generating data on polymorphism in P. falciparum can thus not only speed identification of these key loci but also provide important insight into the evolutionary pressures shaping their function. The most direct route to the needed polymorphism data is through comparative sequencing of genomes of the reference and carefully selected clones. Sequence comparisons between clones with different phenotypes and characteristics will provide critical information about the underlying mechanisms of drug resistance as well as the transmissibility, immunogenicity and virulence of malaria.

Information about the Clones

The specific clones used in this project are as follows:

Clone Origin Drug resistance Other information
Dd2 Indochina CQR, MQR, PYR Parent of genetic cross ARMD phenotype
HB3 Honduras CQS,MQS,PYR Parent of genetic cross
Not ARMD phenotype
Population diversity reference clone

The proposed clones are well suited to meeting the objectives stated above. The Dd2 clone has a high propensity to acquire drug resistance (the ARMD phenotype of Dd2) whereas HB3 does not; complete genomic sequences will make it possible to identify the mutation(s) responsible for this important predisposition to acquiring drug resistance. Moreover, Dd2 and HB3 have provided many leads for drug resistance loci, as their progeny have been maintained and used repeatedly to genetically map drug-resistance determinants by means of microsatellite markers. Leads are generally followed up by sequencing targeted regions of Dd2 and HB3 to identify the particular mutations that may be responsible for the drug resistance. Having the complete genomic sequence of Dd2 and HB3 will make this approach far more efficient.

Photo Captions and Credits

The images on the home page are, from left to right:

  1. This thin film Giemsa stained micrograph depicts a number of ring-form Plasmodium falciparum trophozoites. During the parasite's development, the trophozoite represents an asexual, erythrocytic stage in which the organism looses its "ring" appearance, and begins to accumulate pigment, which is yellow to black in coloration. CDC/ Steven Glenn, Laboratory & Consultation Division.
  2. This thin film Giemsa stained micrograph reveals a mature Plasmodium falciparum schizont. Plasmodium falciparum schizonts have 8 - 24 merozoites, and dark pigment, which is clumped in one mass. Rarely will Maurer's clefts be present, and only then under very specific staining conditions. CDC/ Steven Glenn, Laboratory & Consultation Division.
  3. This thin film blood smear micrograph depicts a Plasmodium falciparum parasite microgametocyte. The Plasmodium falciparum gametocyte is crescent- or sausage-shaped, with a single mass of chromatin, called a macrogametocyte, or, as in this instance, diffuse chromatin which surrounds a dark pigmented mass know as a microgametocyte. CDC/ Dr. Mae Melvin.
  4. Malarial sporozoites develop inside oocysts and are released in large numbers into the hemocoel of Anopheles stephensi mosquitoes. This false-colored electron micrograph shows a sporozoite migrating through the cytoplasm of midgut epithelia. Image by Ute Frevert; false color by Margaret Shear. Source:
  5. The edema exhibited by this African child was brought on by nephrosis associated with malaria. Infection with one type of malaria, Plasmodium falciparum, if not promptly treated, may cause kidney failure. Swelling of the abdomen, eyes, feet and hands are some of the symptoms of nephrosis brought on by the damaged kidneys. CDC/Dr. Myron Schultz