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

Area of Science:

• Genomics
• Parasitology
• Population Genetics

Background:

• Pooled sequencing is cost-effective for genetic variation but limited to small variants.
• Structural variants (SVs) significantly impact genomes and phenotypes but are challenging to study in pooled samples.
• Schistosoma mansoni is a human parasite with complex population genetics.

Purpose of the Study:

• To investigate structural variants (SVs) in laboratory populations of Schistosoma mansoni using long-read pooled sequencing.
• To assess the utility of long-read pooled sequencing for cataloguing SVs and population-specific genetic differences.
• To identify SVs potentially linked to important parasite phenotypes and selection.

Main Methods:

• Generated long-read sequences from pooled Schistosoma mansoni worms (92-152 individuals per population) across five laboratory populations.
• Identified and genotyped 17,446 structural variants (SVs), including deletions, duplications, insertions, inversions, and translocations.
• Analyzed SV distribution, frequency, and association with population-specific traits and genes.

Main Results:

• Identified 17,446 SVs, constituting 6.5% of the genome, enriched in repeat regions.
• Discovered 168 population-specific SVs, with five impacting coding sequences of six genes.
• Found eight SVs with extreme allele frequency differences within quantitative trait loci for drug resistance and larval production.

Conclusions:

• Long-read pooled sequencing is a viable method for cataloguing SVs within populations.
• Population-specific SVs in Schistosoma mansoni may drive adaptation and are linked to important phenotypes.
• This method facilitates rapid assessment of genetic diversity and selection in parasite populations.