Protocol for Hi-C-based identification of chromosomal inversions in mosquitoes

Abstract

Chromosomal inversions play an important role in the genomic evolution and adaptation of mosquito species. Here, we present a protocol for detecting chromosomal inversions in mosquitoes using Hi-C technology and chromatin contact heatmaps. We describe the steps for Hi-C library preparation using the Hi-C Arima+ kit, along with the Arima Library Prep Module, and provide several adaptations for mosquito samples. We then outline procedures for Hi-C data analysis, Hi-C heatmap generation, and the identification of polymorphic and fixed inversions. For additional details on the use and execution of this protocol, please refer to Lukyanchikova et al.1