Population genomics of the filarial nematode parasite Wuchereria bancrofti from mosquitoes

Abstract

Wuchereria bancrofti is a parasitic nematode and the primary cause of lymphatic filariasis – a disease specific to humans. W. bancrofti currently infects over 90 million people throughout the tropics and has been acknowledged by the world health organization as a vulnerable parasite. Current research has focused primarily on the clinical manifestations of disease and little is known about the evolutionary history of W. bancrofti. To improve upon knowledge of the evolutionary history of W. bancrofti, we whole genome sequenced 13 W. bancrofti larvae. We circumvent many of the difficulties of multiple infections by sampling larvae directly from mosquitoes that were experimentally inoculated with infected blood. To begin, we used whole genome data to reconstruct the historical population size. Our results support a history of fluctuating population sizes that can be correlated with human migration and fluctuating mosquito abundances. Next, we reconstructed the putative pedigree of W. bancrofti worms within an infection using the kinship coefficient. We deduced that there are full‐sib and half‐sib relationships residing within the same larval cohort. Through combined analysis of the mitochondrial and nuclear genomes we concluded that this is likely a results of polyandrous mating, the first time reported for W. bancrofti. Lastly, we scanned the genomes for signatures of natural selection. Annotation of putative selected regions identified proteins that may have aided in a parasitic life style or may have evolved to protect against current drug treatments. We discuss our results in the greater context of understanding the biology of an animal with a unique life history and ecology.

Human Migration and the Spread of the Nematode ParasiteWuchereria bancrofti

“…In a previous study of Wb, we used individual Wb worms dissected from mosquitoes but the low infectivity rate of Wb in mosquitoes ( 2%; [Paily et al, 2009]) means that most captured mosquitoes will not contain Wb limiting the number of samples available. However, using whole genome amplification to create sufficient template for sequencing, we showed nucleotide diversity in the sampled population of Papua New Guinea was 0.001 [Small et al, 2016] similar to diversity in populations of O. volvulus [Choi et al, 2016]. However, little else about the history of Wb could be inferred from only the single population.…”

“…The Wb genome sequence (PRJNA275548) was assembled from short reads and contains 5,670 contigs and 5,105 scaffolds [Small et al, 2016]. We used long reads generated with PacBio sequencing to increase the assembly and infer potential chromosome homology with other filarial nematodes.…”

“…We compared these 42 newly sequenced genomes with 13 previously sequenced genomes from Papua New Guinea [Small et al, 2016] and a single genome from Mali [Desjardins et al, 2013]. We removed individuals that were full-siblings as individuals identified in as well as individuals with high heterozygosity across the mitochondrial genome (suggesting that the sequences derive from multiple individuals).…”

“…The program sWGA v0.3.0 [Clarke et al, 2017] was used to design primers for whole-genome amplification of Wb while avoiding amplification of both Human sequences (Hg19) and Wb mitochondrial DNA [Ramesh et al, 2012]. Ten microfilariae (MF) were isolated from each individual blood sample for a total of 200 MF and DNA was isolated following methods in [Small et al, 2016]. After amplification, 42 samples were selected for library preparation and sequencing to include a minimum of 10 samples per geographic location.…”

“…Pac Bio sequencing using chemistry RS II was performed on DNA isolated from the sample(s) described in [Small et al, 2016]. Following whole genome amplification (as noted in [Small et al, 2016]), the whole genome amplified DNA was treated according to methods in [Zhang et al, 2006] to reduce chimeric errors. DNA was cleaned using a 1.6:1 Agencourt AMPure XP bead concentration and then eluted in 20ul ddH2O water.…”