This PDF file includes:

• Supplementary Materials and Methods
  
• section S1. Supplementary Methods
  
• fig. S1. Venn diagram of the protein-coding genes that were annotated in the donkey assembly versus the protein-coding gene annotation for the horse.
  
• fig. S2. Venn diagram of the protein-coding genes that were annotated in the donkey assembly published by Huang et al. (15) versus the protein-coding gene annotation for the E. caballus genome (version EquCab2.0) using Ensembl genes (version 86).
  
• fig. S3. Alignment of horse chromosomes to six donkey scaffolds with putative signs of translocations.
  
• fig. S4. Alignment of donkey scaffolds to corresponding horse chromosomes.
  
• fig. S5. Genetic distance between scaffolds spanning the gap on ECA12 versus the background.
  
• fig. S6. Measured heterozygosity rates for the donkey scaffolds aligned to the various horse chromosomes.
  
• fig. S7. Nei’s genetic distance by windows of 30 kb between donkey and horse chromosomes for scaffolds with signs of inversions.
  
• fig. S8. Effective population size over time by aligning to the horse reference.
  
• fig. S9. Measured heterozygosity rates for the African wild ass using the donkey scaffolds aligned to the horse chromosomes.
  
• table S1. Translocations found between the donkey and horse scaffolds.
  
• table S2. Gene ontologies of biological processes and enriched Reactome pathways associated with genes found in donkey scaffolds with signs of inversions when compared to the horse genome.
  
• table S3. Human phenotypes, human diseases, and pathways associated with genes enriched in detected ROHs.
  
• table S4. Horse sequences used for the detection of donkey scaffolds pertaining to the Y chromosome.
  
• table S5. Heterozygosity rates for various species of asses and zebras computed when aligning to the donkey reference described in this study and recomputed on the basis of the data reported by Jónsson et al. (9), which were aligned to the
  horse reference.
  
• table S6. Listing missing proteins in complete and partially complete Eukaryotic Orthologous Groups from the Core Eukaryotic Genes Mapping Approach.
  
• table S7. Repeat elements and low-complexity DNA sequences masked in the donkey genome using RepeatMasker.
  
• table S8. Repeat elements and low-complexity DNA sequences masked in the donkey genome using the second of the RepeatMasker using the model generated from RepeatModeler as custom library input on the previously masked genome.
  
• table S9. Statistics of the completeness of the different versions of the donkey genome based on 248 Core Eukaryotic Genes.
  
• References (44–62)

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