<i>Var</i> gene nomenclature and generation of a clone tree.

<p>(A) <i>Var</i> gene nomenclature, as defined in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004812#pgen.1004812-Rask1" target="_blank">[8]</a>. From top to bottom: schematic <i>var</i> gene locus, schematic PfEMP1 protein with its DBL & CIDR classes followed by subclasses. Note that the minor domain classes CIDRα4 to α6 and the <i>var2csa</i> specific domains are not represented here. Abbreviations: DBL = Duffy-binding like; CIDR = Cys rich inter-domain region; NTS = N-terminal segment; ATS = Acidic terminal segment. (B) Partial alignment of 3D7 PfEMP1 sequences, representative of the juxtaposition of conserved and variable stretches of amino acids. (C) Principle of generating a clone tree: each blue circle represents a parasite genome, a coloured oval is a mutation, Single Nucleotide Polymorphism (SNP) or Structural variant. Cloning by limiting dilution randomly selects one individual parasite, possibly with one or more mutations. Note that mutations observed in a progeny sample occurred within the parental generation, at some point after the preceding clonal dilution.