Recombination landscape shaped by inversion polymorphisms: a high-density linkage map and chromosome-level assembly of inversion-rich spruce bark beetle genome

Abstract Understanding the recombination landscape is crucial for revealing the extent of its variation across the tree of life and for uncovering its underlying causes and evolutionary consequences. Among the many factors influencing recombination rates, polymorphic inversions are particularly important modifiers. Increasingly, complex inversion landscapes are being documented across diverse taxa, and detailed recombination rate data are essential for advancing our understanding of variation in inversion-rich genomes. Here, we combined whole-genome sequencing of 2 two-generation families with cytogenetic karyotyping to reconstruct a linkage map of the inversion-rich spruce bark beetle (Ips typographus) genome. Our results revealed a different chromosome number than previously reported (15AA + Xy) and a recombination landscape strongly shaped by the inversion landscape. The total length of the autosomal, sex-averaged map was 978 cM, with an overall mean recombination rate of 4.9 cM/Mb. Recombination was spatially heterogeneous across the genome and was significantly reduced in parents heterozygous for specific inversion arrangements. We also used the linkage map to upgrade the existing genome assembly to chromosome level, correcting previous misassemblies (often associated with inversions), revising inversion size estimates, identifying new putative inversions, and updating repeat content. Notably, inversions were found to be depleted in transposable elements. These findings provide a valuable foundation for future research on this important forest pest and offer broader insights into how recombination landscapes are shaped in inversion-rich genomes.