Pooled, Long-read Sequencing for Structural Variant Characterization in Schistosome Populations

Pooled sequencing provides a rapid cost-effective approach to assess genetic variation segregating within populations of organisms. However, such studies are typically limited to single nucleotide variants and small indels (≤50 bp), and have not been used for structural variants (SVs > 50 bp) which impact large portions of most genomes and may significantly impact phenotype. Here, we examined SVs circulating in five laboratory populations of the human parasite Schistosoma mansoni by generating long-read sequences from pools of worms (92-152 per population). We were able to identify and genotype 17,446 SVs, representing 6.5% of the genome despite challenges in identifying low-frequency variants. SVs included deletions (n = 8,525), duplications (n = 131), insertions (n = 8,410), inversions (n = 311), and translocations (n = 69) and were enriched in repeat regions. More than half (59%) of the SVs were shared between ≥4 populations, but 12% were found in only one of the five populations. Within this subset, we identified 168 population-specific SVs that were at-or-near fixation (>95% alternate allele frequency) in one population but missing (<5%) in the other four populations. Five of these variants impact the coding sequence of six genes. We also identified eight SVs with extreme allele frequency differences between populations within quantitative trait loci for biomedically important pathogen phenotypes (drug resistance, larval stage production) identified in prior genetic mapping studies. These results demonstrate that long-read sequence data from pooled individuals is a viable method to quickly catalogue SVs circulating within populations. Furthermore, some of these variants may be responsible for, or linked to, regions experiencing, population-specific directional selection.