Additional file 1 of Genomic evidence for recurrent genetic admixture during the domestication of Mediterranean olive trees (Olea europaea L.)
Creators: name: Julca, Irene
name: Marcet-Houben, Marina
name: Cruz, Fernando
name: Gómez-Garrido, Jèssica
name: Gaut, Brandon S.
name: Díez, Concepción M.
name: Gut, Ivo G.
name: Alioto, Tyler S.
name: Vargas, Pablo
name: Gabaldón, Toni
Publisher: name: figshare
Year: 2020
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1 Fig. S1. Genome comparison of sylvestris and europaea. (a) Cumulative genome length per scaffold ranked in order of size for the genome assembly of europaea (Oe9 - green, Oe6 - olive, picual - orange) and sylvestris (blue). A straight vertical line represents a perfect genome assembly. The horizontal plateaus indicate many small scaffolds. The top right end of each curve shows the total number of scaffolds. (b) Syntenic plot of the genome of europaea against sylvestris generated by SynMap. (c) Histogram of log 10 transformed Ks values of syntenic gene pairs identified as calculated by SynMap. Fig. S2. Plastid genome of the cultivar Farga. Protein coding genes are shown in green, rRNAs in light blue, and tRNAs in purple. The SNPs are shown per each individual sequenced in this study in the following order starting from outside: ‘Arbequina’, ‘Picual’, ‘Beladi’, ‘Sorani’, ‘Koroneiki’, ‘Frantoio’, ‘Lechin de Granada’, ‘Lechin de Sevilla’, ‘Megaritiki’, ‘Chemlal de Kabilye’, sylvestris-T, sylvestris-S. Fig. S3. Mitochondrial genome of the cultivar Farga. Protein coding genes are shown in green, rRNAs in light blue, and tRNAs in purple. The SNPs are shown per each individual sequenced in this study in the following order starting from outside: ‘Arbequina’, ‘Picual’, ‘Beladi’, ‘Sorani’, ‘Koroneiki’, ‘Frantoio’, ‘Lechin de Granada’, ‘Lechin de Sevilla’, ‘Megaritiki’, ‘Chemlal de Kabilye’, sylvestris-T, sylvestris-S. Fig. S4. Homozygous SNP distribution along the nuclear genome. The SNPs are shown in windows of 100 Kb. Cultivars are plotted in green and sylvestris in blue. Since cv. Farga was used as a reference genome, we do not expect homozygous SNPs for this sample. Fig. S5. Heterozygous SNP distribution along the nuclear genome. The SNPs are shown in windows of 100 Kb. Cultivars are plotted in green and sylvestris in blue. Fig. S6. Principal component analysis (PCA) based on 24,724,756 nuclear SNPs. The first two principal components (PC1 and PC2) are plotted, which explained 35.17% and 11% of the total variance, respectively. The individuals are shown with three different colors according to the results of structure (Fig. 2b): blue for individuals composed mainly of cluster 1, green for individuals composed mainly of cluster 2, and orange for mixed individuals. The cultivars are identified by a circle and the oleaster by a cross (x). Fig. S7. Patterns of introgression. (a) D statistics across the largest scaffold (Oe9_LG02) in windows of 5Kb and step size of 1Kb for the analysis of the trios: ‘Beladi’-‘Dokkar’-sylvestris-S, ‘Beladi’-‘Chemlal de Kabilye’-sylvestris-S’, ‘Beladi’-‘Megaritiki’-sylvestris-S, ‘Beladi’-‘Menya’-sylvestris-S, ‘Beladi’-‘Lianolia Kerkyras’-sylvestris-S. The horizontal red line marks D = 0.5. (b) Genomic regions introgressed with a D &gt; 0.5 in ‘Megaritiki’ (grey), ‘Menya’ (blue), ‘Lianolia Kerkyras’ (orange), ‘Dokkar’ (green), and ‘Chemlal de Kabilye’ (red). Percentages below the cultivar names represent the percentage of the genomic region that is introgressed in the cultivar. Fig. S8. Number of homozygous and heterozygous SNPs (SNPs/Kb) in the intergenic, intronic and coding region of the genome. The coding region was divided according to the changes that the allele can produce (synonymous and nonsynonymous). Fig. S9. Derived site frequency spectrum (SFS) of synonymous, four fold degenerate, non-synonymous, and deleterious SNPs. (a) Wild populations, (b) Cultivars_set1, (c) Cultivars_set2. Subspecies cuspidata was used as an outgroup for identifying the derived allele.