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.