Structural variation drives praziquantel response and host adaptation in Schistosoma japonicum

Description

Structural variation (SVs) represents a major yet underappreciated source of genomic diversity that shapes parasite adaptation and evolution. Here, we generated the first comprehensive SV map of S. japonicum from 72 genomes across six endemic regions in Asia, identifying 12,632 high-confidence SVs that affect 3.55% of the S. japonicum genome and define population structure and adaptive trajectories.

Steps to reproduce

Refer to the protocol for SV calling (https://github.com/Shuhua-Group/SVanalysis_STARProtocols), for each sample, SVs discovered by Manta, Lumpy, and CNVnator were merged using svimmer. Then, all SVs detected in all samples were merged again by svimmer with the same filters. Lastly, population-scale genotyping was performed using Graphtyper2, and only results based on the aggregate model were retained.

Institutions

• Fudan University

  Shanghai, Shanghai

Categories

Funders

• National Natural Science Foundation of China

  Beijing, China

  Grant ID: 32030020
• National Key Research and Development Program of China

  Grant ID: 2023YFC2605400
• National Natural Science Foundation of China

  Beijing, China

  Grant ID: 32288101
• National Natural Science Foundation of China

  Beijing, China

  Grant ID: 32470649
• Shanghai Science and Technology Commission Program

  Grant ID: 23JS1410100
• National Key Research and Development Program of China

  Grant ID: 2021YFC2300802
• Shanghai Science and Technology Commission Program

  Grant ID: QNKJ2024023

Licence