Data for: Pangenome analysis reveals local adaptation to climate driven by introgression in oak species

The genetic basis of local adaptation has been extensively studied in
natural populations. However, a comprehensive genome-wide perspective on
the contribution of structural variants (SVs) and adaptive introgression
to local adaptation remains limited. In this study, we performed de
novo assembly and annotation of 22 representative accessions of
Quercus variabilis, identifying a total of 543,372 SVs. These SVs
play crucial roles in shaping genomic structure and influencing gene
expression. By analysing range-wide genomic data, we identified
both SNPs and SVs associated with local adaptation in Q.
variabilis and Q. acutissima. Notably, SV-outliers
exhibit selection signals that did not overlap with SNP-outliers,
indicating that SNP-based analyses may not detect the same candidate genes
associated with SV-outliers. Remarkably, 29−37% of candidate SNPs
were located in a 250 kb region on chromosome 9, referred to as Chr9-ERF.
This region contains eight duplicated ethylene-responsive
factor (ERF) genes, which may have contributed to local
adaptation of Q. variabilis and Q. acutissima. We also found that
a considerable number of candidate SNPs were shared between Q.
variabilis and Q. acutissima in the
Chr9-ERF region, suggesting a pattern of repeated selection. We
further demonstrated that advantageous variants in this region were
introgressed from western populations of Q. acutissima into Q.
variabilis, providing compelling evidence that introgression facilitates
local adaptation. This study offers a valuable genomic resource for future
studies on oak species and highlights the importance of pan-genome
analysis in understanding mechanisms driving adaptation and evolution.