A Network Approach to Analyzing Highly Recombinant Malaria Parasite Genes

Abstract

The var genes of the human malaria parasite Plasmodium falciparum present a challenge to population geneticists due to their extreme diversity, which is generated by high rates of recombination. These genes encode a primary antigen protein called PfEMP1, which is expressed on the surface of infected red blood cells and elicits protective immune responses. Var gene sequences are characterized by pronounced mosaicism, precluding the use of traditional phylogenetic tools that require bifurcating tree-like evolutionary relationships. We present a new method that identifies highly variable regions (HVRs), and then maps each HVR to a complex network in which each sequence is a node and two nodes are linked if they share an exact match of significant length. Here, networks of var genes that recombine freely are expected to have a uniformly random structure, but constraints on recombination will produce network communities that we identify using a stochastic block model. We validate this method on synthetic data, showing that it correctly recovers populations of constrained recombination, before applying it to the Duffy Binding Like-α (DBLα) domain of var genes. We find nine HVRs whose network communities map in distinctive ways to known DBLα classifications and clinical phenotypes. We show that the recombinational constraints of some HVRs are correlated, while others are independent. These findings suggest that this micromodular structuring facilitates independent evolutionary trajectories of neighboring mosaic regions, allowing the parasite to retain protein function while generating enormous sequence diversity. Our approach therefore offers a rigorous method for analyzing evolutionary constraints in var genes, and is also flexible enough to be easily applied more generally to any highly recombinant sequences.

Author Summary

The human malaria parasite kills nearly 1 million people each year globally. Frequent genetic exchange between malaria parasites creates enormous genetic diversity that largely explains the lack of an effective vaccine for the disease. Traditional phylogenetic tools cannot accommodate this type of diversity, however, and rigorous analytical tools capable of making sense of gene sequences that recombine frequently are still lacking. Here, we use network techniques that have been developed by the physics and network science communities to analyze malaria parasite gene sequences, allowing us to automatically identify highly variable mosaic regions in sequence data and to derive the network of recombination events. We apply our method to seven fully-sequenced parasite genomes, and show that our method provides new insights into the complex evolutionary patterns of the parasite. Our results suggest that the structure of these sequences allows the parasite to rapidly diversify to evade immune responses while maintaining antigen structure and function.