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

## Description of the data and file structure

There are two zipped files here: one contains all the codes for this analysis, and the other is the VCF file of SV and SNP calling used for this analysis.

### File: Code.zip

All scripts were put in the file \"src\".

#### Part 1: pan-genome analyses

1.1. assembly.sh

```
1) For the reference individual

2) For the other pan-genome individual
```

1.2. repeat elements.sh

```
1) For the reference individual

2) For the other pan-genome individual
```

1.3. annotations.sh

1.4. Pangenome_graph.sh

```
1) RUN PBSV for SV calling

2) RUN SVIM for SV calling

3) RUN Sniffles for SV calling

4) RUN cuteSV for SV calling

5) RUN SVIMasm for SV calling

6) RUN Assemblytics for SV calling

7) RUN merge SVs for SV calling

8) RUN winnowmap for SNP calling

9) RUN deepvariant for indel calling

10) Construct the Pan-genome Graph
```

1.5 Collin...,