Additional file 1 of Origin and diversity of Capsella bursa-pastoris from the genomic point of view

Additional file 1: Fig. S1. Scheme for data acquisition for the genetic map. Fig. S2. An example of a contig fragment with a colored state of the markers. Due to the low coverage some of the markers are "noisy". Fig. S3. An example of chimeric assembly. Two adjacent markers located at a distance of ~90 kbp have 33 "recombinations" per 100 chromosomes, which is impossible and indicates independent inheritance of markers.Fig. S4. An example of correction of a local chimeric assembly. a Insertion of a foreign fragment(s) and b view of the site after correction. The green dashed lines show the signals indicating the proximity of the sites. Fig. S5. Simulation of the subgenome separation procedure. Example of the coverage by reads of the parental species of some reference contigs created from the genomes of C. orientalis and C. rubella for subgenome separation. Fig. S6. Analysis of introgression by admixture analysis in C. bursa-pastoris, for K=6. The colors of the line names correspond to the populations in Fig. 4b.Fig. S7. Fbranch matrix plotted using Dsuite f4-statistics results for different tree topologies of parental species and lineages of C. bursa-pastoris for subgenome O. a for ((((ME,EU),ASI),Co),Cgr-Outgroup) tree; b for ((((ASI,EU),ME),Co),Cgr-Outgroup) tree; c for ((((ASI,ME),EU),Co),Cgr-Outgroup) tree; d for (((ME,EU),ASI),Co-Outgroup) tree; e for (((ASI,EU),ME),Co-Outgroup) tree; f for (((ASI,ME),EU),Co-Outgroup) tree. Co – C. orientalis, Cgr – C. rubella/C. grandiflora, and ASI, ME, EU – lineages of C. bursa-pastoris. Fig. S8. Fbranch matrix plotted using Dsuite f4-stastics results for different tree topologies of parental species and lineages of C. bursa-pastoris for subgenome R. a for ((((ME,EU),ASI),Cgr),Co-Outgroup) tree; b for ((((ASI,EU),ME),Cgr),Co-Outgroup) tree; c for ((((ASI,ME),EU),Cgr),Co-Outgroup) tree; d for (((ME,EU),ASI),Cgr-Outgroup) tree; e for (((ASI,EU),ME),Cgr-Outgroup) tree; f for (((ASI,ME),EU),Cgr-Outgroup) tree. Co – C. orientalis, Cgr – C. rubella/C. grandiflora, and ASI, ME, EU – lineages of C. bursa-pastoris. Fig. S9. F2 data processing. Fig. S10. Building the SNP Database