Landscape genomics reveals genetic signals of environmental adaptation of African wild eggplant

# Landscape genomics reveals genetic signals of environmental adaptation of African wild eggplant ## Description of the data and file structure **File list:** * Wild African eggplant SNP dataset.vcf * Wild African eggplant sample details and environmental data.csv ## **Data specific information** 1\. Wild African eggplant SNP dataset\.vcf The data lines in the .vcf file include * CHROM - chromosome: An identifier from the reference genome * POS - position: The reference position, with the 1st base having position 1. Positions are sorted numerically, in increasing order, within each reference sequence CHROM * ID - identifier: Colon-separated list of unique identifiers for the SNPs * REF - reference base(s) * ALT - alternate base(s): A list of alternate non-reference alleles. * QUAL - quality: Phred-scaled quality score for the assertion made in ALT * FILTER - filter status: PASS if this position has passed all filters, i.e., a call is made at this position * INFO - additional information * The genotype names e.g. aethiopicum1 are the accessions used in the analysis. The names are derived from the species names followed by a number denoting the sequence of the genotype in the order of the species. The genotype, even within the same species, maybe from different populations. Further information about the genotypes is found in the following file. 2\. Wild African eggplant sample details and environmental data\.csv * Number of genotypes (rows): 153 * Genotype details (rows 1-7): Genotype: sequencing code; VINO: variety identification number at the WorldVeg genebank in Taiwan; Taxon: genotype name derived from the species name and a sequential number in the list (same as the genotype names on the vcf file); lon: longitude; lat: latitude; Country: Country ISO codes for the country of origin of the accessions. The country codes include: TZA- Tanzania, KEN- Kenya, UGA- Uganda, SDN- Sudan, NGA- Nigeria, and GHA- Ghana. * Number of environmental variables: 10 PDrM\_14: Precipitation of the driest month (mm); PWaQ\_18: Precipitation of the warmest quarter (mm); PCoQ\_19: Precipitation of the coldest quarter (mm); MTWeQ\_8: Mean temperature of the wettest quarter (°C); srad: solar radiation (kJ m-2 day-1); phh2o: pH of the soil water (pH \* 10); nitrogen: soil nitrogen content (cg/kg); clay: soil clay content (g/kg); silt: soil silt content (g/kg); ocd: organic carbon deposit (hg/m3). *** ## Sharing/Access information This is a section for linking to other ways to access the data, and for linking to sources the data is derived from, if any. Data was derived from the following sources: * WorlClim 2.1 climate data for 1970-2000 (Fick & Hijmans, 2017) at a resolution of 2.5 minutes (https://www.worldclim.org/data/worldclim21.html) * SoilGrids database released in 2016 ([https://soilgrids.org/](https://soilgrids.org/)) through ISRIC—WDC Soils (Hengl et al., 2017) at 250-meter resolution and at a depth of 15-30 cm ## Code/Software