Wang, Zhenyue, Li, Ying, Sun, Pengchuan, Zhu, Mingjia, Wang, Dandan, Lu, Zhiqiang, Hu, Hongyin, Xu, Renping, Zhang, Jin, Ma, Jianxiang, Liu, Jianquan, and Yang, Yongzhi
Additional file 1: Fig. S1. The previously reported topologies within eudicots. Fig. S2. 19-Kmer-based analysis to estimate the genome size of Buxus austro-yunnanensis. Fig. S3. Interaction frequency distribution of Hi-C links among chromosomes. Fig. S4. GC contents of five early-diverging eudicot species. Fig. S5. BUSCO results for six eudicots. Fig. S6. LTR insertion time of Buxus austro-yunnanensis. Fig. S7. Gene structures of Aquilegia, Buxus, Nelumbo, Trochodendron and Tetracentron. Fig. S8. The phylogenetic trees of the nuclear sequences with concatenated and coalescence-based methods. Fig. S9. Divergence times of the 28 species. Fig. S10. The phylogenetic tree of the chloroplast dataset. Fig. S11. Quartet score of each node based on the nuclear gene trees. Fig. S12. Superimposed ultrametric gene trees in a consensus DensiTree plot. Fig. S13. Relative importance of incomplete lineage sorting (ILS), gene tree estimation error (Est. error), and hybridization in generating gene tree variation. Fig. S14. Collinear gene dot plots between Buxus austro-yunnanensis and Aristolochia, Aquilegia, Nelumbo, Tetracentron, Cercidiphyllum, Vitis. Fig. S15. Collinear gene dot plots between Cercidiphyllum, Vitis and Simmondsia, Carthamus, Olea. Fig. S16. Merged dotplot of Aquilegia, Buxus, Nelumbo, Trochodendron, Tetracentron and Vitis. Fig. S17. Heatmap of cluster of collinearity relationships in Aquilegia (aco), Buxus austro-yunnanensis (byu), Nelumbo (nnu), Trochodendron (tar), Tetracentron (tsi) and Vitis (vvi). Fig. S18. Demonstration of pieces of AEK 1 in Aquilegia (aco), Buxus austro-yunnanensis (byu), Nelumbo (nnu), Trochodendron (tar), Tetracentron (tsi) and Vitis (vvi). Fig. S19. Demonstration of pieces of AEK 2 in Aquilegia (aco), Buxus austro-yunnanensis (byu), Nelumbo (nnu), Trochodendron (tar), Tetracentron (tsi) and Vitis (vvi). Fig. S20. Demonstration of pieces of AEK 3 in Aquilegia (aco), Buxus austro-yunnanensis (byu), Nelumbo (nnu), Trochodendron (tar), Tetracentron (tsi) and Vitis (vvi). Fig. S21. Demonstration of pieces of AEK 4 in Aquilegia (aco), Buxus austro-yunnanensis (byu), Nelumbo (nnu), Trochodendron (tar), Tetracentron (tsi) and Vitis (vvi). Fig. S22. Demonstration of pieces of AEK 5 in Aquilegia (aco), Buxus austro-yunnanensis (byu), Nelumbo (nnu), Trochodendron (tar), Tetracentron (tsi) and Vitis (vvi). Fig. S23. Demonstration of pieces of AEK 6 in Aquilegia (aco), Buxus austro-yunnanensis (byu), Nelumbo (nnu), Trochodendron (tar), Tetracentron (tsi) and Vitis (vvi). Fig. S24. Demonstration of pieces of AEK 7 in Aquilegia (aco), Buxus austro-yunnanensis (byu), Nelumbo (nnu), Trochodendron (tar), Tetracentron (tsi) and Vitis (vvi). Fig. S25. Comparison between the previous AEK (PAEK) and our constructed AEK. Fig. S26. Karyotype projection of Aquilegia, Nelumbo, Buxus austro-yunnanensis, Tetracentron, Trochodendron and Coffea genome based on PAEK. Fig. S27. Karyotype projection of Vitis and Cercidiphyllum based on PAEK and AEK. Fig. S28. Karyotype projection of Aquilegia, Nelumbo, Buxus austro-yunnanensis, Tetracentron, Trochodendron and Coffea genome based on AEK. Fig. S29. Collinear gene dot plots and karyotype projection between Cercidiphyllum and Bretschneidera, Theobroma, Acer, Averrhoa, Populus, Tripterygium. Fig. S30. Collinear gene dot plots and karyotype projection between Cercidiphyllum and Cucumis, Phaseolus, Malus, Betula, Eucalyptus, Vitis. Fig. S31. Collinear gene dot plots and karyotype projection between Cercidiphyllum and Coffea, Ipomoea, Olea, Apium, Carthamus, Davidia, Rhododendron, Simmondsia. Fig. S32. Collinear gene dot plots and karyotype projection between Coptis and Aquilegia, Cercidiphyllum and Muscadinia, Vitis and Muscadinia. Fig. S33. Collinear gene dot plots and karyotype projection between Tetracentron and Trochodendron. Fig. S34. Synteny comparison among asterids species with Davidia as reference. Fig. S35. Synteny comparison among rosids species with Tripterygium as reference. Table S1. The detail sequencing information of Buxus austro-yunnanensis. Table S2. Summary of genome assembly. Table S3. Contig N50 values of the early-diverging eudicots. Table S4. Summary of chromosome level assembly. Table S5. Statistic of repetitive elements in the assembled genome. Table S6. Comparison of gene space of Buxus austro-yunnanensis with other genomes. Table S7. Assessment of the predicted genes by BUSCO (database: eudicotyledons_odb10). Table S8. Functional annotation of the predicted genes. Table S9. Summary of the 28 species genome that used in this study. Table S10. Average total introgression proportion per species pair in QuIBL analysis. Table S11. The QuIBL analysis result.