Developing an Automated Panel Design Tool for SNP-Based Targeted Amplicon Sequencing of Schistosoma mansoni Populations

Abstract

Genomic surveillance of Schistosomiasis across endemic regions could provide insights into the efficacy of current control strategies and allow the impact of selection on the parasite genome to be monitored, providing early warning of the emergence of anthelmintic resistance. Studies exploring this require large numbers of samples yet even with decreasing costs for sequencing, it is still prohibitively expensive to sequence whole genomes of large samples of individuals from populations. Targeted amplicon sequencing is a feasible approach to sequencing from populations while excluding possible contaminating sequences and allowing the generation of genome variation data at a reasonable depth and reduced costs. This study introduces an approach to target SNP-rich sites across the parasite’s genome to contribute to molecular marker discovery and analysis in studying natural Schistosoma populations. Here, an automated tool has been created for flexible amplicon panel design, to enable targeted sequencing of Schistosoma mansoni populations. Using an in silico targeted amplicon data set generated from available (unpublished) whole-genome sequencing data for 574 population genetics samples from different geographic regions, the panels designed from the software showed ability to distinguish parasites from geographically unrelated parasites. This automated panel design approach, when validated, will facilitate the quick generation of panels and support application in endemic countries and regions where high-throughput genome sequencing is not readily available. In turn, the approach and software will enable research on targeted sequencing in Schistosoma mansoni populations.