Additional file 3 of The spinach YY genome reveals sex chromosome evolution, domestication, and introgression history of the species

Additional file 3. Supplementary tables. Table S1. Sequencing information of “Cornell-NO.9” (YY) genome. Table S2. Comparison of contig assemblies among three genomes of Spinacia accessions. Table S3. Statistics of Hi-C mapping of “Cornell-NO.9” (YY) genome. Table S4. Assembly and annotation evaluation in S. oleracea cultivar “Cornell-NO.9” (YY) and “Viroflay” (XX) genomes. Table S5. TE annotation of S. oleracea cultivar “Cornell-NO. 9” (YY) and “Viroflay” (XX) genomes. Table S6. Summary of sequencing statistics and sex phenotypes (F: female; M: male) in F1 population. Table S7. Summary of genes identified from SDR (MSY) and X-counterpart. Table S8. Gene information of sex-determination region (SDR) of Y chromosome. Table S9. Gene information of X-counterpart of SDR in X chromosome. Table S10. Statistics summary of Pacbio reads mapping onto junction regions of structure variations within SDR. Table S11. SDR genes having sex-biased expression during flower development. Table S12. Expression of genes that are mentioned in proposed sex-determination/differentiation pathway. Table S13. Accessions of spinach S. oleracea and wild sibling species used for resequencing and population genomics as well as sex-chromosome analyses. Table S14. Details of genes in a swept region with strong selection signals on Chr3:106112216-108343948. Table S15. D statistic values of ABBA-BABA tests for different geographical regions of S. oleracea and wild species. Table S16. Introgression loci with strong signals from S. tetrandra, S. turkestanica and India cultivars respectively. Table S17. Primers used in qRT-PCR for validating the expression patterns of key candidate genes found in this study [123–132].

附加文件3：补充附表
附表S1：“Cornell-NO.9（YY）”基因组的测序信息
附表S2：3份菠菜（Spinacia）种质基因组的重叠群组装结果比较
附表S3：“Cornell-NO.9（YY）”基因组的Hi-C染色质构象捕获（Hi-C）作图统计数据
附表S4：菠菜（Spinacia oleracea）栽培种“Cornell-NO.9（YY）”与“Viroflay（XX）”基因组的组装与注释评估结果
附表S5：菠菜（Spinacia oleracea）栽培种“Cornell-NO.9（YY）”与“Viroflay（XX）”基因组的转座因子（transposable element, TE）注释信息
附表S6：F1群体的测序统计汇总及性别表型（F：雌性；M：雄性）
附表S7：从性别决定区（sex-determination region, SDR；MSY）及其X染色体对应区域（X-counterpart）中鉴定到的基因统计
附表S8：Y染色体性别决定区（sex-determination region, SDR）的基因信息
附表S9：X染色体上性别决定区（sex-determination region, SDR）的X染色体对应区域的基因信息
附表S10：PacBio测序读段比对至性别决定区（sex-determination region, SDR）内结构变异连接区域的统计汇总
附表S11：花发育过程中具有性别偏向表达的性别决定区（sex-determination region, SDR）基因
附表S12：所提出的性别决定/分化通路中提及基因的表达数据
附表S13：用于重测序、群体基因组学及性染色体分析的菠菜（Spinacia oleracea）及其野生近缘种的种质材料信息
附表S14：3号染色体Chr3:106112216-108343948区域内携带强选择信号的选择清扫区域的基因详细信息
附表S15：菠菜（Spinacia oleracea）不同地理类群及野生种的ABBA-BABA检验统计值
附表S16：分别来自四籽菠菜（Spinacia tetrandra）、土耳其菠菜（Spinacia turkestanica）及印度栽培品种的具有强渐渗信号的基因位点信息
附表S17：用于验证本研究中关键候选基因表达模式的实时定量逆转录PCR（quantitative real-time reverse transcription PCR, qRT-PCR）所用引物序列[123–132]