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Additional file 1: Table S1. Statistics of the transcriptome assemblies for species of the Maculipennis Group. Table S2. Genes of An. atroparvus used as markers for detection of interspecies chromosome rearrangements on the X chromosome in five species of the Maculipennis Subgroup. Table S3. Mosquito species and sampling sites. Figure S1. A phylogenetic analysis of ortholog groups split into 4 equally-sized datasets based on the length of the alignments after trimal filtration. Figure S2. A phylogenetic analysis using whole-genome datasets from six Anopheles species.

Table S1. Genes harboring rare pathogenic variants revealed in exomes of patients with TBE (cases set) and in exomes of the control individuals (control set). Table S2. Cases_only set, containing genes that were unique for the cases set. Table S3. Genetic variants (SNPs or Indels) associated with severe forms of TBE at P-value less than 0.01. Table S4. Three sets of genes harboring genetic variants associated with severe forms of TBE at P-value less than 0.01: (1) associated set; (2) associated_possibly damaging set; (3) associated_harmful set. Table S5. Genetic variants found in eighty genes shared by the cases_only (2407 genes) set and the associated_possibly damaging set (132 genes). Table S6. ECM proteoglycans - cell periphery set, containing genes from the cases_only set, annotated by overrepresented terms. Table S7. PPIs between genes/proteins from the ECM proteoglycans - cell periphery set and genes/proteins from the TBEVHostDB. Table S8. The list of 154 genes/proteins from the ECM proteoglycans - cell periphery set, that were involved in PPIs network with genes/proteins from TBEVHostDB and their N indexes. Table S9. PPI interactions involving 15 top genes/proteins from the ECM proteoglycans - cell periphery set with Nâ >â 3. References were checked manually by reviewing the literature. Table S10. PPI interactions involving 5 genes/proteins from the associated_harmful set. References were checked manually by reviewing the literature. (DOCX 13 kb)

Figure S1. Results of Principal Component Analysis (PCA) for Hereford and Kazakh Whiteheaded breeds. Figure S2. Q-Q plots for GWA analyses. Figure S3. Distribution of haploblock lengths. Figure S4. Number of haplotypes in haploblocks. (DOCX 4181 kb)

Supplemental Methods. Further details of species identification using mtDNA consensus mapping method; raw read filtering criteria; genome size estimation using K-mer analysis; leopard genome assembly using various K-mer values; repeat annotation; species selection for comparative genomic analysis. (DOCX 43 kb)

Species and sub-species identification for three leopard samples. Figure S2. Distribution of K-mer frequency in the error-corrected reads. Figure S3. GC content distributions. Figure S4. Composition of mammalian orthologous genes. Figure S5. Divergence time estimation of 18 mammals. Figure S6. Contraction of the amylase gene families (AMY1 and AMY2) in carnivores. Figure S7. Frame-shift mutations in Felidae GCKR genes. Figure S8. Felidae-specific amino acid changes in DNA repair system. Figure S9. Felidae-specific amino acid change in MEP1A protein. Figure S10. Felidae-specific amino acid change in ACE2 protein. Figure S11. Felidae-specific amino acid change in PRCP protein. (DOCX 2024 kb)

Species and sub-species identification for three leopard samples. Figure S2. Distribution of K-mer frequency in the error-corrected reads. Figure S3. GC content distributions. Figure S4. Composition of mammalian orthologous genes. Figure S5. Divergence time estimation of 18 mammals. Figure S6. Contraction of the amylase gene families (AMY1 and AMY2) in carnivores. Figure S7. Frame-shift mutations in Felidae GCKR genes. Figure S8. Felidae-specific amino acid changes in DNA repair system. Figure S9. Felidae-specific amino acid change in MEP1A protein. Figure S10. Felidae-specific amino acid change in ACE2 protein. Figure S11. Felidae-specific amino acid change in PRCP protein. (DOCX 2024 kb)

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)

Comparison of orthogroup size distribution between the current de novo assembly for Atlantic salmon, at each stage of filtering, relative to Atlantic salmon reference genome proteins (GCF_000233375.4). (PDF 57Â kb)

Distribution of orthologs in the current Atlantic salmon de novo assembly compared to the distribution of orthologs in the NCBI Atlantic salmon RefSeq protein dataset (GCF_000233375.1). OrthoFinder results were filtered to retain only OrthoGroups with at least one RefSeq salmon protein present. (PDF 228Â kb)

NCBI SRA and TSA accessions for raw read data and assemblies (respectively), for all four species. (PDF 58Â kb)

GO analysis performed on the subsets of â species-specificâ transcripts for each of the four assemblies. (PDF 34Â kb)

GO analysis performed on the subsets of â species-specificâ transcripts for each of the four assemblies. (PDF 34Â kb)

Distribution of orthologs in the current Atlantic salmon de novo assembly compared to the distribution of orthologs in the NCBI Atlantic salmon RefSeq protein dataset (GCF_000233375.1). OrthoFinder results were filtered to retain only OrthoGroups with at least one RefSeq salmon protein present. (PDF 228Â kb)

Comparison of orthogroup size distribution between the current de novo assembly for Atlantic salmon, at each stage of filtering, relative to Atlantic salmon reference genome proteins (GCF_000233375.4). (PDF 57Â kb)

Comparison of full-length transcript reconstruction between the four current assemblies and three previously published transcriptomes; Magnanou et al.â s Arctic charr assembly [34], and the PhyloFish DB brown trout and European whitefish assemblies [35]. Cumulative number of unique matching proteins that aligned to the NCBI protein database for Atlantic salmon (GCF_000233375.1) at a given coverage: Atlantic salmon (yellow), brown trout (green), Arctic charr (blue), European whitefish (red), Magnanou et al. Arctic charr transcriptome (black), PhyloFish brown trout (dark grey), and PhyloFish European whitefish (light grey). (PDF 35Â kb)

Number and proportion of gene ontology annotations assigned to each speciesâ transcriptome. (PDF 246Â kb)

Comparison of full-length transcript reconstruction between the four current assemblies and three previously published transcriptomes; Magnanou et al.â s Arctic charr assembly [34], and the PhyloFish DB brown trout and European whitefish assemblies [35]. Cumulative number of unique matching proteins that aligned to the NCBI protein database for Atlantic salmon (GCF_000233375.1) at a given coverage: Atlantic salmon (yellow), brown trout (green), Arctic charr (blue), European whitefish (red), Magnanou et al. Arctic charr transcriptome (black), PhyloFish brown trout (dark grey), and PhyloFish European whitefish (light grey). (PDF 35Â kb)

NCBI SRA and TSA accessions for raw read data and assemblies (respectively), for all four species. (PDF 58Â kb)