Additional file 2 of Genomic evidence for recurrent genetic admixture during the domestication of Mediterranean olive trees (Olea europaea L.)

Additional file 2 Table S1. General characteristics of the four genome assemblies of the cv. Farga (Oe6, Oe9), picual, and the genome assembly of the var. sylvestris from Turkey. Table S2. Total percentage of reads mapped from two RNAseq libraries, as well as, percentage of unique mappings to the Oe9 and picual genomes. Table S3. List of unique genes of europaea and sylvestris with their homologous function. Table S4. General characteristics of the plastid and mitochondrial genomes of the cultivar Farga. Table S5. Admixture coefficient (Q) of each individual per cluster. This table was used to create the Fig. 2b. Table S6. Introgressed regions per each cultivar. Columns in order show: cultivar name (‘Chemlal de Kabilye’, ‘Megaritiki’, ‘Lianolia Kerkyras’, ‘Menya’, and ‘Dokkar’), scaffold, start of the region, end of the region, D-statistic, genes present in the region. Table S7. Number of synonymous, nonsynonymous, four fold degenerate, affecting stop codons, affecting start codons SNPs for homozygous and heterozygous positions per individual. TheπN/πS ratio of homozygous SNPs, πN/πS ratio of heterozygous SNPs, and πN/πS ratio of total number of SNPs is also shown. Table S8. Number of proteins with SNPs and with nonsynonymous SNPs per individual. Table S9. GO terms enriched in the list of proteins that do not have a nonsynonymous SNP. First column shows the term category, the second, the GO term, the third, the term level, the fourth, the p-value, and the fifth, the term name. Table S10. List of genes with negative Tajima’s D. The columns in order indicate: the group of cultivars (cultivars_set1 or cultivars_set2), gene, scaffold, number of SNPs, Tajima’s D. Table S11. Result of McDonald and Kreitman test for all coding regions of wild vs cultivars_set1 and wild vs cultivars_set2. Table S12. Result of McDonald and Kreitman test for each gene. The columns in order show: the comparison for the test (wild vs cultivars_set1 or wild vs cultivars_set2), number of fixed nonsynonymous sites (Fn), number of fixed synonymous sites (Fs), number of polymorphic nonsynonymous sites (Pn), number of polymorphic synonymous sites (Ps), the ratio of fixed nonsynonymous sites per synonymous sites (Fn/Fs), the ratio of polymorphic nonsynonymous sites per synonymous sites (Pn/Ps), the neutrality index (NI), p-value (Fisher’s exact tests), homologous function. Table S13. Derived site frequency of synonymous, nonsynonymous, deleterious, and four fold degenerate sites. The p-values using the Mann-Whitney U test of the comparison of neutral and no neutral sites are also shown. Table S14. Selective sweeps for cultivars_set1 and cultivars_set2. The genes that are present in the regions are indicated. Table S15. List of proteins in regions with selected sweeps and their associated function. Table S16. Blast results of the 19 genes of sylvestris-T against cv. Farga. The results were filtered by %identity > 90 and e-value<1e-5. Asterisk mark genes with negative values of Tajima’s D in cultivars_set1 (*), in cultivars_set2 (**), and in both sets of cultivars (***). Table S17. Selective sweeps present in introgressed regions of ‘Chemlal de Kabilye’, ‘Megaritiki’, ‘Lianolia Kerkyras’, and ‘Menya’. Table S18. D-statistic of all trios of subsp. europaea analysed. The columns show the name of the individual 1, individual 2, individual 3, D-statistic, p-value, and adjusted p-value.