Additional file 1 of Cotton pan-genome retrieves the lost sequences and genes during domestication and selection

Additional file 1: Table S1. Summary of genomic sequencing data of 1961 cottons in this study. Table S2. Summary of SNP filtering in 1913 G. hirsutum, G. barbadense and other Gossypium species accessions for each chromosome. Table S3. Summary of InDels filtering in 1913 accessions for each chromosome. Table S4. Summary of SNP filtering in 1623 G. hirsutum accessions for each chromosome. Table S5. Summary of SNP and InDel filtering in 261 G. barbadense accessions for each chromosome. Table S6. The SNP and InDel annotation of subpopulation. Table S7. The number of structural variations filtered by four steps in each subpopulation. Table S8. Summary of copy number variations for each chromosome in different subpopulation. Table S9. The SNP-based domestication sweeps and covering genes. Table S10. The SNP-based improvement signals and covering genes. Table S11. Continuously selected signals and genes during domestication and improvement. Table S12. The CNV-based domestication signals and overlapped SNP-based signals. Table S13. The CNV-based improvement signals and overlapped SNP-based signals. Table S14. Significant SNP-based GWAS signals for 15 agronomic traits. Table S15. Summary of snpQTLs that overlapped with domestication and improvement signals. Table S16. Summary of pleiotropic snpQTLs in multiple panels. Table S17. Summary of pleiotropic cnvQTLs in 419 panel accessions. Table S18. Summary of cnvQTLs that overlap with domestication and improvement signals. Table S19. Summary of assembly non-reference contigs between G. hirsutum and G. barbadense. Table S20. Filtering non-reference sequences following several filtering steps. Table S21. Protein-coding genes predicted in the G. hirsutum non-reference genome. Table S22. Protein-coding genes predicted in the G. barbadense non-reference genome. Table S23. Summary of PacBio reads and Illumina reads for 10 representative G. hirsutum cotton accessions. Table S24. Summary of polished contigs for 10 representative G. hirsutum accessions and draft genomes mapped to the GhPangenome. Table S25. Meta-genome likely assembly for landrace, American and modern cotton variety groups. Table S26. Selected PAVs during cotton domestication. Table S27. Selected PAVs during cotton improvement. Table S28. Selected PAVs during both domestication and improvement. Table S29. Summary of selective regions and covering genes during domestication and improvement. Table S30. Detail information of functional SNP variation in landrace and two geographic groups. Table S31. Summary of PAVs associated with QTLs.

附加文件1：表S1 本研究中1961份棉花的基因组测序数据汇总。
表S2 1913份陆地棉（Gossypium hirsutum）、海岛棉（Gossypium barbadense）及其他棉属（Gossypium）材料各染色体的单核苷酸多态性（Single Nucleotide Polymorphism, SNP）过滤汇总。
表S3 1913份材料各染色体的插入缺失（Insertion-Deletion, InDel）过滤汇总。
表S4 1623份陆地棉材料各染色体的单核苷酸多态性过滤汇总。
表S5 261份海岛棉材料各染色体的单核苷酸多态性与插入缺失过滤汇总。
表S6 亚群体的单核苷酸多态性与插入缺失注释信息。
表S7 各亚群体经四轮过滤得到的结构变异数量。
表S8 不同亚群体各染色体的拷贝数变异（Copy Number Variation, CNV）汇总。
表S9 基于单核苷酸多态性的驯化选择区域及覆盖基因。
表S10 基于单核苷酸多态性的改良选择信号及覆盖基因。
表S11 驯化与改良过程中持续受到选择的信号与基因。
表S12 基于拷贝数变异的驯化选择信号及与单核苷酸多态性选择信号的重叠情况。
表S13 基于拷贝数变异的改良选择信号及与单核苷酸多态性选择信号的重叠情况。
表S14 15个农艺性状的基于单核苷酸多态性的全基因组关联分析（Genome-Wide Association Study, GWAS）显著信号。
表S15 与驯化及改良信号重叠的单核苷酸多态性数量性状基因座（Quantitative Trait Locus, QTL）汇总。
表S16 多个关联群体中的多效性单核苷酸多态性数量性状基因座汇总。
表S17 419份材料关联群体中的多效性拷贝数变异数量性状基因座汇总。
表S18 与驯化及改良信号重叠的拷贝数变异数量性状基因座汇总。
表S19 陆地棉与海岛棉间的非参考组装重叠群汇总。
表S20 经多轮过滤后的非参考序列汇总。
表S21 陆地棉非参考基因组中预测的蛋白编码基因。
表S22 海岛棉非参考基因组中预测的蛋白编码基因。
表S23 10份代表性陆地棉材料的PacBio读长与Illumina读长汇总。
表S24 10份代表性陆地棉材料的抛光重叠群及比对至陆地棉泛基因组的草图基因组汇总。
表S25 地方品种、美国品种与现代棉花品种类群的宏基因组初步组装结果。
表S26 棉花驯化过程中受到选择的存在/缺失变异（Presence-Absence Variation, PAV）。
表S27 棉花改良过程中受到选择的存在/缺失变异。
表S28 棉花驯化与改良过程中均受到选择的存在/缺失变异。
表S29 驯化与改良过程中的选择性区域及覆盖基因汇总。
表S30 地方品种与两个地理类群的功能性单核苷酸多态性变异详细信息。
表S31 与数量性状基因座相关的存在/缺失变异汇总。