The genomic architecture of introgression during <i>Rhododendron</i> speciation

Summary Understanding how genomic architecture shapes patterns of gene flow is fundamental to unraveling the mechanisms of plant speciation. Here, we investigate whether differential gene flow dynamics between genomic spatial compartments play a role in speciation of Rhododendron subsect. Scabrifolia . We first present a chromosome‐level genome assembly for Rhododendron spinuliferum , and use this to characterize large‐scale chromatin organization, including A and B compartments. We then use genome resequencing data for 139 individuals from 15 populations of all eight species of R . subsect. Scabrifolia endemic to Southwest China to investigate speciation history. We find significant disparities in the extent of genomic differentiation between A and B compartments. The B compartment, closely associated with centromeres, tends to exhibit higher genetic differentiation, whereas the gene‐rich A compartment appears less differentiated and exhibits more extreme f dm values, suggesting more extensive localized introgression. We propose that the heterogeneous nature of gene flow across genomic compartments contributes to speciation in Rhododendron , and may play a critical yet underappreciated role in gene flow dynamics in plants.