Introgression can be an important source of new alleles for adaption under rapidly changing environments, perhaps even more important than standing variation. Though introgression has been extensively studied in many plants and animals, key questions on the underlying mechanisms of introgression still remain unanswered. In previous study by studying introgression between populations of two widespread sympatric Asian oak species, we found introgression between two species is determined not only by the genetic distance but also by the similarity of the environments in which they live—populations occupying similar ecological sites tended to exchange same genomic regions. And we found introgressed genes often have more conservative expression levels between two species. To further investigate the mechanisms of introgression in entire genus Quercus L., we constructed a graph pangenome of oaks. This pangenome included 9 reference-level genome assemblies, which served as an unbiased reference for constructing a phylogeny tree based on 69 oak species. We meticulously computed the introgression regions within the genomes of these species, revealing a multitude of introgression events within the Quercus L. genus. We also generated high-quality multiomics genomic resources, including resequencing, ATAC-sequencing, WGBS and transcriptome sequencing, for 18 oak species and 2 other Fagaceae species sampled in multiple forests of China. Furthermore, we correlated the introgression patterns with the whole-genome methylation map and chromatin accessibility map, suggesting a potential link between epigenetic modifications and introgression. Our results provide new avenues of research for revealing the mechanisms by which introgression occurs among closely related species. Keywords：introgression, Quercus, pangenome.
When and how did introgression happen? A pan-genomic multiomics study of Genus Quercus L.