DOI: 10.6084/m9.figshare.30586995
title: Additional file 1 of Pangenomic structural variant patterns reflect evolutionary diversification in Brassica napus

description: Additional file 1. Supplementary Tables. Supplementary Table 1. List of 94 ecogeographically diverse rapeseedaccessions selected from the ERANET-ASSYST diversity set. Supplementary Table 2. Summary of long-read DNA resequencing data by Oxford Nanopore Technology for 94 B. napus accessions. Supplementary Table 3. Genome assembly statistics for 94 B. napus accessions. Supplementary Table 4. Number of removed SVs in each chromosome in the process of filtering-out SVs that are likely to overlap with a deleted chromosome segment. Supplementary Table 5. Number of removed SVs in the process of filtering-out SVs that are likely to overlap a deleted chromosome segment. Supplementary Table 6. Number of SVs called for each B. napus accession by aligning long-reads to Darmor-bzh v10 reference genome. Supplementary Table 7. Number of total SVs called for each subgenome of B. napus accession by aligning long reads to Darmor-bzh v10 reference genome. Supplementary Table 8. Overview of pangenome-wide distribution and frequency of collective SVs in B. napus. Supplementary Table 9. Overview of genes intersecting pangenome-wide collective SVs in B. napus. Supplementary Table 10. Overview of putative flowering-time-related genes intersecting pangenome-wide collective SVs in B. napus.  Supplementary Table11. Overview of putative R genes intersecting pangenome-wide collective SVs in B. napus. Supplementary Table 12. Number of inversions called for each B. napus accession by aligning reference-guided genome assemblies to Darmor-bzh v10 reference genome. Supplementary Table 13. Overview of pangenome-wide distribution and frequency of inversions in B. napus. Supplementary Table 14. Overview of distribution and frequency of over-represented or under-represented inversion events across B. napus pangenome for different ecotype groups. Supplementary Table 15. Fisher’s test analysis for distribution and statistical association by ecotype groups for over-represented or under-represented inversion events across B. napus pangenome. Supplementary Table 16. Overview of collective SV hotspots across B. napus pangenome. Supplementary Table 17. Overview of inversion hotspots across B. napus pangenome. Supplementary Table 18. FST Values for pairwise comparison of swede versus non-swede accessions using pangenome-wide collective SVs in B. napus. Supplementary Table 19. FST Values for pairwise comparison of East Asian OSR versus all other OSR accessions using pangenome-wide collective SVs. Supplementary Table 20. FST Values for pairwise comparison of WOSR versus SOSR accessions using pangenome-wide collective SVs. Supplementary Table 21. Overview of putative genes intersecting genomic regions under selection for pairwise comparison of swede versus non-swede accessions using pangenome-wide collective SVs. Supplementary Table 22. Overview of putative genes intersecting genomic regions under selection for pairwise comparison of East Asian OSR versus all other OSR accessions using pangenome-wide collective SVs. Supplementary Table 23. Overview of putative genes intersecting genomic regions under selection for pairwise comparison of WOSR versus SOSR accessions using pangenome-wide collective SVs. Supplementary Table 24. GO enrichment analysis for genes overlapping with genomic regions under selection for pairwise comparison of swede versus non-swede accessions for pangenome-wide collective SVs. Supplementary Table 25. GO enrichment analysis for genes overlapping with genomic regions under selection for pairwise comparison of East Asian OSR versus all other OSR accessions for pangenome-wide collective SVs. Supplementary Table 26. GO enrichment analysis for genes overlapping with genomic regions under selection for pairwise comparison of WOSR versus SOSR accessions for pangenome-wide collective SVs. Supplementary Table 27. FST Values for pairwise comparison of swede versus non-swede accessions using pangenome-wide inversions in B. napus. Supplementary Table 28. FST Values for pairwise comparison of East Asian OSR versus all other OSR accessions using pangenome-wide inversions. Supplementary Table 29. FST Values for pairwise comparison of WOSR versus SOSR accessions using pangenome-wide inversions. Supplementary Table 30. Overview of putative genes intersecting genomic regions under selection for pairwise comparison of swede versus non-swede accessions using pangenome-wide inversions. Supplementary Table 31. Overview of putative genes intersecting genomic regions under selection for pairwise comparison of East Asian OSR versus all other OSR accessions using pangenome-wide inversions. Supplementary Table 32. Overview of putative genes intersecting genomic regions under selection for pairwise comparison of WOSR versus SOSR accessions using pangenome-wide inversions. Supplementary Table 33. GO enrichment analysis for genes overlapping with genomic regions under selection for pairwise comparison of swede versus non-swede accessions for pangenome-wide inversions. Supplementary Table 34. GO enrichment analysis for genes overlapping with genomic regions under selection for pairwise comparison of East Asian OSR versus all other OSR accessions for pangenome-wide inversions. Supplementary Table 35. GO enrichment analysis for genes overlapping with genomic regions under selection for pairwise comparison of WOSR versus SOSR accessions for pangenome-wide inversions. Supplementary Table 36. Overlapping regions of pangenome-wide collective SVs and inversions under selection in swede versus non-swede comparison. Supplementary Table 37. Overlapping regions of pangenome-wide collective SVs and inversions under selection in Asian OSR versus all other OSR comparison. Supplementary Table 38. Overlapping regions of pangenome-wide collective SVs and inversions under selection in WOSR versus SOSR comparison. Supplementary Table 39. Overview of pangenome-wide distribution and frequency of gene presence-absence variation in B. napus. Supplementary Table 40. Overview of pangenome-wide gene presence-absence that correlate with WOSR, SOSR, East Asian OSR, or swede group of accessions.