Additional file 3 of Genome structure variation analyses of peach reveal population dynamics and a 1.67 Mb causal inversion for fruit shape

Additional file 3: Supplementary Tables S8–S9, S13, S15–S23. This file contains the supplementary tables referenced in the main text. Table S8. Information about Lovell and Rui You Pan1 (RYP1). Table S9. Specific PAVs for the RYP1 and Lovell v2.0 genomes. Table S13. Basic information and statistics of 186 re-sequenced peach accessions (including 149 P. persica and 37 P. kansuensis) used in this study. Table S15. PCR validation of randomly selected SVs. Table S16. Enriched gene ontology (GO) terms with coding or upstream (< 1 kb) regions (putative promoters) affected by SVs. Table S17. The SVs occurred in gene cluster of receptor-like protein kinase gene LRK10 in the three consecutive SV hotspots. Table S18. Highly divergent SVs during peach improvement. Table S19. SNPs significantly associated with flat fruit shape. Table S20. InDels significantly associated with flat fruit shape. Table S21. SVs significantly associated with flat fruit shape. Table S22. Summary information for SNPs of 126 accessions identified in this study with genotyped SNPs from customized SNP genotyping array. Table S23. PCR or qRT-PCR primers used in this study.

附加文件3：补充表S8~S9、S13、S15~S23。本文件包含正文中引用的补充表格。
表S8：Lovell与芮友潘1号（RYP1）相关信息
表S9：RYP1与Lovell v2.0基因组的特异性存在/缺失变异（Presence/Absence Variation，PAV）
表S13：本研究使用的186份桃重测序种质的基本信息与统计数据（包含149份普通桃（Prunus persica）与37份甘肃桃（Prunus kansuensis））
表S15：随机选取的结构变异（Structural Variation，SV）的PCR验证结果
表S16：受SV影响的编码区或上游（<1kb）区域（推定启动子）的富集基因本体（Gene Ontology，GO）术语
表S17：三个连续SV热点区域中类受体蛋白激酶基因LRK10基因簇内出现的SV
表S18：桃改良过程中高度分化的SV
表S19：与果实扁平性状显著关联的单核苷酸多态性（Single Nucleotide Polymorphism，SNP）
表S20：与果实扁平性状显著关联的插入缺失变异（Insertion/Deletion，InDel）
表S21：与果实扁平性状显著关联的SV
表S22：本研究鉴定的126份桃种质的SNP分型汇总信息，该分型基于定制化SNP基因分型芯片完成
表S23：本研究使用的PCR或实时定量PCR（quantitative real-time PCR，qRT-PCR）引物