Additional file 1 of Genomic legacy of the African cheetah, Acinonyx jubatus

Supplemental figures. Figure S1. Cheetah genome size estimation by 17-mers. Figure S2. Depth distribution of cheetah reads. Figure S3. GC content and average sequencing depth values. Figure S4. Depth distribution of re-sequencing reads. Figure S5. Distribution of syntenic blocks in genome windows. Figure S6. Ten largest cat-cheetah rearrangements. Figure S7. Size of homozygosity stretches in Felidae genomes. Figure S8. Ideograms of homozygosity regions. Figure S9. Comparison of cheetah and human MHC regions. Figure S10. Comparison of cheetah and dog MHC regions. Figure S11. Inferred historical population sizes by PSMC analysis. Figure S12. Bootstrap values for DaDi demographic models. Figure S13. Alignments of the AKAP4 gene. Figure S14. Evolutionary history of LDH gene families. Figure S15. Cumulative distribution of 36-mers. Figure S16. Copy-number distribution in control regions. Figure S17. Example of fixed duplications on scaffold606. (PDF 2027 kb)