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.

附加文件2 表S1：‘Farga’栽培品种（cv. Farga，Oe6、Oe9）、‘Picual’栽培品种的4个基因组组装体，以及土耳其来源的野生油橄榄变种（var. sylvestris）的基因组组装体的基本特征。表S2：两个RNA测序（RNAseq）文库的比对测序读段总占比，以及唯一比对到Oe9和‘Picual’基因组的测序读段占比。表S3：欧洲油橄榄（europaea）与sylvestris变种的特有基因列表及其同源功能注释。表S4：‘Farga’栽培品种的质体基因组与线粒体基因组的基本特征。表S5：每个个体在各聚类中的祖源混合系数（Q值），该表用于绘制图2b。表S6：各栽培品种的渐渗区域。列依次为：栽培品种名称（‘Chemlal de Kabilye’、‘Megaritiki’、‘Lianolia Kerkyras’、‘Menya’及‘Dokkar’）、支架序列（scaffold）、区域起始位点、区域终止位点、D统计量（D-statistic）、该区域包含的基因。表S7：每个个体的纯合与杂合位点的同义突变、非同义突变、四价简并位点、影响终止密码子的突变、影响起始密码子的单核苷酸多态性位点（SNPs）数量；同时给出纯合SNPs的πN/πS比值、杂合SNPs的πN/πS比值以及总SNPs的πN/πS比值。表S8：每个个体中携带SNPs及携带非同义SNPs的蛋白质数量。表S9：无非义SNPs的蛋白质列表所富集的基因本体（GO）术语。第一列为术语类别，第二列为GO术语，第三列为术语层级，第四列为p值，第五列为术语名称。表S10：携带负塔伊马D统计量（Tajima’s D）的基因列表。列依次为：栽培品种组（cultivars_set1或cultivars_set2）、基因名称、支架序列（scaffold）、SNPs数量、塔伊马D统计量（Tajima’s D）。表S11：野生型与cultivars_set1、野生型与cultivars_set2的所有编码区的麦克唐纳-克里特曼检验（McDonald and Kreitman test，MK检验）结果。表S12：每个基因的麦克唐纳-克里特曼检验结果。列依次为：检验对比组（野生型 vs cultivars_set1 或野生型 vs cultivars_set2）、固定非同义位点数量（Fn）、固定同义位点数量（Fs）、多态性非同义位点数量（Pn）、多态性同义位点数量（Ps）、固定非同义位点与同义位点的比值（Fn/Fs）、多态性非同义位点与同义位点的比值（Pn/Ps）、中性指数（NI）、p值（费舍尔精确检验）、同源功能注释。表S13：同义位点、非同义位点、有害位点以及四价简并位点的衍生等位基因频率；同时给出中性位点与非中性位点比较的曼-惠特尼U检验（Mann-Whitney U test）p值。表S14：cultivars_set1与cultivars_set2的选择性清除（selective sweeps）区域，标注该区域包含的基因。表S15：携带选择性清除区域的蛋白质列表及其相关功能注释。表S16：土耳其来源sylvestris变种的19个基因与‘Farga’栽培品种的BLAST比对结果。筛选条件为序列一致性百分比（%identity）>90%且期望值（e-value）<1e-5。星号标记在cultivars_set1中携带负塔伊马D统计量值的基因（*）、在cultivars_set2中携带负塔伊马D统计量值的基因（**），以及在两组栽培品种中均携带负塔伊马D统计量值的基因（***）。表S17：‘Chemlal de Kabilye’、‘Megaritiki’、‘Lianolia Kerkyras’及‘Menya’的渐渗区域中存在的选择性清除。表S18：所有分析的欧洲油橄榄亚种（subsp. europaea）三重样本组合的D统计量结果。列依次为：个体1名称、个体2名称、个体3名称、D统计量（D-statistic）、p值以及校正后p值。