A protocol for applying low-coverage whole-genome sequencing data in structural variation studies
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Updated: Jul 23, 2025

Following the Dynamics of Structural Variants in Experimentally Evolved Populations
Published on: February 3, 2023
1State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 201203, China.
Abstract:
Structural variations (SVs) have a great impact on various biological processes and influence physical traits in many species. Here, we present a protocol for applying the low-coverage next-generation sequencing data of Rhipicephalus microplus to detect high-differentiated SVs accurately. We also outline its use to investigate population/species-specific genetic structures, local adaptation, and transcriptional function. We describe steps for constructing variation maps and SV annotation. We then detail population genetic analysis and differential gene expression analysis. For complete details on the usage and execution of this protocol, please refer to Liu et al. (2023).
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