Whole genome amplification and exome sequencing of archived schistosome miracidia

Abstract

Adult schistosomes live in the blood vessels and cannot easily be sampled from humans, so archived miracidia larvae hatched from eggs expelled in feces or urine are commonly used for population genetic studies. Large collections of archived miracidia on FTA cards are now available through the Schistosomiasis Collection at the Natural History Museum (SCAN). Here we describe protocols for whole genome amplification of Schistosoma mansoni and Schistosome haematobium miracidia from these cards, as well as real time PCR quantification of amplified schistosome DNA. We used microgram quantities of DNA obtained for exome capture and sequencing of single miracidia, generating dense polymorphism data across the exome. These methods will facilitate the transition from population genetics, using limited numbers of markers to population genomics using genome-wide marker information, maximising the value of collections such as SCAN.

Snail-Related Contributions from the Schistosomiasis Consortium for Operational Research and Evaluation Program Including Xenomonitoring, Focal Mollusciciding, Biological Control, and Modeling

“…The difficulty of obtaining schistosomes other than highly bottlenecked/inbred laboratory strains has made the SCAN collection very attractive to global research groups working on comparative genomics, with a number of studies in high-profile journals already published using specimens from SCORE and other programs archived in SCAN. 66 – 68 Schistosomiasis Collections at the Natural History Museum has also been available to support other projects working in schistosomiasis-endemic regions 16 , 69 and to facilitate secondary usage of collections. Although SCAN continues to be a very successful extension of the SCORE program, complications related to implementation of the Nagoya Protocol to the Convention on Biological Diversity may make sharing of genetic samples more challenging in the future, and ways need to be found to facilitate the best research outcomes toward disease elimination at all times, not only during pandemic emergencies.…”

Parasite Population Genetic Contributions to the Schistosomiasis Consortium for Operational Research and Evaluation within Sub-Saharan Africa

“… 33 , 34 Additional refinements developed through SCORE studies and beyond now allow repeat analyses on unamplified genomic DNA, cost-effectively and without genome amplification bias, thereby improving data quality and giving the potential for greater analytical depth. 35 , 36 Such new methodologies and refinements allow an enormous reduction in the logistical effort required in assaying parasite populations. Furthermore, these methodologies can be applied to natural schistosome populations across continents, allowing wide-scale genetic and genomic analyses of schistosome populations over space and time, and encompasses all life stages from adult worms to free-living miracidia and cercariae (e.g., refs.…”

Ancient hybridization and introgression of an invadolysin gene in schistosome parasites

“…We used whole genome amplification of single miracidia dried on FTA cards followed by exome capture and sequencing (Illumina 2500) following methods described in 12 . In addition to exome capture, whole-genome sequence data was generated for twelve samples, six from each population (Niger and Zanzibar).…”

“…To investigate this natural hybridization at the genomic level, we collected S. haematobium eggs, from human urine samples, and hatched miracidia. We sequenced exomes from 96 miracidia (1 per patient) from Niger (n=48) and Zanzibar (n=48) using whole genome amplification and exome capture (Data S1; Fig S1; 12) . Initial attempts to genotype mitochondrial loci contained within the exome probe set failed in 31 of the Nigerien S. haematobium samples.…”

“…The presence of S. bovis mitochondria in Nigerien S. haematobium could result from contemporary hybridization or past introgression events. To differentiate between these two scenarios, we examined 370,770 autosomal, exonic (single nucleotide polymorphisms) SNPs 12,14 recovered by the exome capture probes. In addition to our 96 S. haematobium samples we used sequence data from six closely-related schistosome species in the S. haematobium species group (S. bovis, S. curassoni, S. intercalatum, S. guineensis, S. mattheei, and S. margrebowiei) generated in previous studies 15,16 .…”