Local adaptation in the Patagonian foundation tree species Nothofagus pumilio

Npumilio_specific_candidate_genes.xlsx 

Study-specific candidate genes. For annotation information on the 1,789 candidate genes from orthogroups, see Milesi at al 2023 (https://doi.org/10.1101/2023.01.05.522822 and Supplemental Tables S12-S14).
Contains contig, Uniprot-TAIR code and original species, and reason for inclusion in the candidate list (e.g. upregulated or downregulated in the heat stress-transcriptome study (https://doi.org/10.1371/journal.pone.0246615), or of interest for wood growth)
The list includes some duplicate contigs that are contained in the candidate gene set; they were left in for the "Reason" information
N_pumilio_06Nov2019_probe_coverage.txt

Probe design file as provided by IGA Technology Services
All called SNP variants. Data for 502 individual tree samples are included: 496 adult trees + 6 replicates.

variants-gatk_haplotypecaller_SNP_raw.vcf.gz are raw called variants.
variants-gatk_haplotypecaller_SNP.vcf.gz are coarsely quality-filtered and are the starting datasets for our downstream analyses.
Npumilio_IDs_vcforder_all_info.xlsx

Metadata for all samples in the .vcf files (in the same order), including site name, geographic coordinates and elevation
Npumilio_orthogroups.csv

Orthogroups, TAIR codes, and best-hit Nothofagus contigs for cross-referencing with orthogroup candidate gene set (Milesi at al 2023 (https://doi.org/10.1101/2023.01.05.522822 and Supplemental Tables S12-S14)).