Additional file 1: Figure S1. of The wolf reference genome sequence (Canis lupus lupus) and its implications for Canis spp. population genomics

Phylogenies. The left panel shows the phylogenetic tree of all the samples, estimated from reads that are mapped to the boxer dog reference genome, while the right panel shows the phylogenetic tree estimated from the data after mapping reads to the denovo assembled wolf reference genome. Figure S2. Distribution of repeat elements. Total amount of bases in different repeat classes across the two reference genomes. Figure S3. Comparison of the divergence of the different repeat elements from their consensus sequence. The top panel shows the total number of bases against the divergence from the consensus sequence in each repeat family when using the de novo wolf reference genome for alignment. The bottom panel shows the same figures when using the boxer reference genome. Figure S4. Principal Components Analysis (PCA). Panels A and B show the first four principal components of the genotypes when using the de novo wolf reference assembly. For making these PCA plots, we used a missingness cutoff of 0.9 and a minor allele frequency cutoff of 0.2. Panels C and D show the first four principal components of the genotypes when using the boxer reference genome while using the same filtering thresholds. Figure S5. Picture of the skull of the Swedish wolf sample used for reference genome assembly. Table S1. Coverage and heterozygosity estimates. The coverage and heterozygosity are shown for each sample included in the study. For each animal, the higher estimate of coverage are bolded. (PDF 1652 kb

Additional file 2 of Genomic legacy of the African cheetah, Acinonyx jubatus

Supplemental tables. Table S1. Sequenced cheetah reads for de novo genome assembly. Table S2. Re-sequenced cheetah reads for population analyses. Table S3. Estimated cheetah genome size. Table S4. Cheetah genome assembly information. Table S5. Reference-assisted assembly of cheetah chromosomes. Table S6. RepeatMasker results for transposable elements in carnivore genomes. Table S7. Total length of repeat regions in cheetah. Table S8. Tandem repeats in five carnivore genomes. Table S9. Complex tandem repeat families. Table S10. Protein-coding gene annotation. Table S11. Non-coding RNA annotation. Table S12. Nuclear mitochondrial genes. Table S13. Lengths of cheetah synteny blocks. Table S14. Cheetah rearrangements. Table S15. Called SNV statistics. Table S16. SNV effects by impact. Table S17. SNV effects by functional class. Table S18. SNV effects by genomic region. Table S19. SNV locations relative to genes. Table S20. SNV distribution in cheetah genome. Table S21. SNV distribution in tiger genomes. Table S22. SNV locations and effects in coding genes of Felidae genomes. Table S23. SNV counts in genes in domestic cat and tigers. Table S24. SNV counts in genes in cheetahs. Table S25. Nucleotide diversity in mitochondrial genomes of mammals. Table S26. Nucleotide diversity in MHC class I and II genes. Table S27. Demographic models and their log-likelihood values. Table S28. Population data by DaDi. Table S29. Reproductive system genes with identified function. Table S30. Filtration of cheetah reproduction system genes. Table S31. Nucleotide diversity of masked assemblies. Table S32. Statistics on autosomal segmental duplications. (PDF 127 kb

Additional file 3 of Genomic legacy of the African cheetah, Acinonyx jubatus

Supplemental datasheets. Datasheet S1. List of cheetah-specific de novo predicted genes with functional domains annotated by InterPro scan. Datasheet S2. List of gene families in eight mammal species identified by protein homology. Datasheet S3. Results of gene family expansion and contraction analysis. Datasheet S4. CAFE results from gene family contraction and expansion analysis. Datasheet S5. Results of gene selection analysis. Datasheet S6. Reproductive system genes with damaging mutations. Datasheet S7. Segmental duplication genes. Datasheet S8. List of reproductive genes with segregated high effect mutations and corresponding genotypes of cheetah. (XLSX 711 kb