Next Generation Semiconductor Based Sequencing of the Donkey (Equus asinus) Genome Provided Comparative Sequence Data against the Horse Genome and a Few Millions of Single Nucleotide Polymorphisms.
Authors: Bertolini Francesca, Scimone Concetta, Geraci Claudia, Schiavo Giuseppina, Utzeri Valerio Joe, Chiofalo Vincenzo, Fontanesi Luca
Journal: PloS one
Summary
# Editorial Summary Donkeys have historically received minimal genomic investigation compared to horses, limiting our understanding of breed diversity and genetic health in the species. Francesca Bertolini's team sequenced complete genomes from two individual donkeys using Ion Proton semiconductor sequencing and screened pooled DNA from three Italian breeds (Grigio Siciliano, Ragusano and Martina Franca) using reduced representation libraries, then cross-referenced all data against both a donkey draft genome and the well-characterised horse genome (EquCab2.0). The research identified approximately 4.8 million single nucleotide polymorphisms (SNPs) in donkeys, with nucleotide divergence between horses and donkeys calculated at 0.52–0.57%; notably, certain autosomal regions and the entire X chromosome showed markedly low divergence, suggesting evolutionary conservation of functionally important sequences across equid species. A notably high SNP density clustered in regions homologous to horse chromosome 12, which is recognised in equine literature as harbouring frequent copy number variants—a finding that warrants further investigation in donkey populations. For practitioners, this SNP resource provides the foundational genetic markers necessary to establish parentage verification systems, monitor genetic diversity within endangered donkey breeds, and identify breed-specific or health-related variants, ultimately supporting more informed breeding programmes and conservation strategies for donkey populations.
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Practical Takeaways
- •This SNP resource enables genetic testing and population monitoring for donkey breed conservation and parentage verification programs.
- •Identified genetic markers can support selective breeding decisions in donkey populations by providing objective genomic data on breed diversity and genetic relationships.
- •The comparative genomic data between horses and donkeys provides a foundation for investigating breed-specific genetic traits and disease susceptibilities in donkeys using genomic tools.
Key Findings
- •Nucleotide divergence between horse and donkey genomes was approximately 0.52-0.57%, with conserved regions identified across autosomal chromosomes and chromosome X that may be evolutionarily important in equids.
- •Approximately 4.8 million single nucleotide polymorphisms (SNPs) were identified and annotated in the donkey genome using combined next-generation sequencing data from multiple platforms.
- •Y-chromosome variants were identified that could be useful for tracking donkey paternal lineages and establishing genetic monitoring systems for donkey breed conservation.