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PloS one2015; 10(7); e0131925; doi: 10.1371/journal.pone.0131925

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.

Abstract: Few studies investigated the donkey (Equus asinus) at the whole genome level so far. Here, we sequenced the genome of two male donkeys using a next generation semiconductor based sequencing platform (the Ion Proton sequencer) and compared obtained sequence information with the available donkey draft genome (and its Illumina reads from which it was originated) and with the EquCab2.0 assembly of the horse genome. Moreover, the Ion Torrent Personal Genome Analyzer was used to sequence reduced representation libraries (RRL) obtained from a DNA pool including donkeys of different breeds (Grigio Siciliano, Ragusano and Martina Franca). The number of next generation sequencing reads aligned with the EquCab2.0 horse genome was larger than those aligned with the draft donkey genome. This was due to the larger N50 for contigs and scaffolds of the horse genome. Nucleotide divergence between E. caballus and E. asinus was estimated to be ~ 0.52-0.57%. Regions with low nucleotide divergence were identified in several autosomal chromosomes and in the whole chromosome X. These regions might be evolutionally important in equids. Comparing Y-chromosome regions we identified variants that could be useful to track donkey paternal lineages. Moreover, about 4.8 million of single nucleotide polymorphisms (SNPs) in the donkey genome were identified and annotated combining sequencing data from Ion Proton (whole genome sequencing) and Ion Torrent (RRL) runs with Illumina reads. A higher density of SNPs was present in regions homologous to horse chromosome 12, in which several studies reported a high frequency of copy number variants. The SNPs we identified constitute a first resource useful to describe variability at the population genomic level in E. asinus and to establish monitoring systems for the conservation of donkey genetic resources.
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Publication Date: 2015-07-07 PubMed ID: 26151450PubMed Central: PMC4495037DOI: 10.1371/journal.pone.0131925Google Scholar: Lookup
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  • Non-U.S. Gov't

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The study discusses the sequencing of the genome of two male donkeys, breaking down the gaps in research around donkeys at a genomic level. The comparative sequence data against the horse genome and the identification of millions of Single Nucleotide Polymorphisms offer potential insights into the diversity of the donkey population and can be a valuable resource in the conservation of their genetic resources.

Research Methods and Objective

  • The team sequenced the genome of two male donkeys with the help of the next-generation semiconductor-based sequencing platform, the Ion Proton sequencer.
  • They compared the obtained sequence information with the official draft of the donkey genome and Illumina reads from which it was derived.
  • The team also made comparisons against EquCab2.0, which is the assembly of the horse genome.
  • The Ion Torrent Personal Genome Analyzer was used to sequence Reduced Representation Libraries (RRL) from a DNA pool that includes different breeds of donkeys (Grigio Siciliano, Ragusano, and Martina Franca).

Findings

  • The number of next-generation sequencing reads aligned with the EquCab2.0 horse genome exceeded those aligned with the draft donkey genome because the horse genome had a larger N50 for contigs and scaffolds.
  • They estimated a ~0.52-0.57% nucleotide divergence between horses (E. caballus) and donkeys (E. asinus). There were regions with low nucleotide divergence in several autosomal chromosomes and the whole chromosome X, which might be important in equids evolution.
  • Comparing Y-chromosome regions, they identified variants valuable in tracking donkey paternal lineages.
  • About 4.8 million single nucleotide polymorphisms (SNPs) in the donkey genome were identified. This was done by combining sequencing data from Ion Proton (whole genome sequencing), Ion Torrent (RRL), and Illumina reads. A higher density of SNPs was present in regions homologous to horse chromosome 12, known for high frequency of copy number variants.

Implication of the Study

  • The identification of millions of SNPs is crucial as it gives the ability to describe the variability at the genomic level in the E. asinus species.
  • This pool of information can be used to track paternal lineage and potentially save endangered donkey species and breeds, essentially aiding in the conservation of the genetic resources of donkeys.

Cite This Article

APA
Bertolini F, Scimone C, Geraci C, Schiavo G, Utzeri VJ, Chiofalo V, Fontanesi L. (2015). 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. PLoS One, 10(7), e0131925. https://doi.org/10.1371/journal.pone.0131925

Publication

PloS one
ISSN: 1932-6203
NlmUniqueID: 101285081
Country: United States
Language: English
Volume: 10
Issue: 7
Pages: e0131925

Researcher Affiliations

Bertolini, Francesca
  • Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, Bologna, Italy; Department of Veterinary Sciences, Animal Production Unit, University of Messina, Polo Universitario dell'Annunziata, Messina, Italy.
Scimone, Concetta
  • Department of Veterinary Sciences, Animal Production Unit, University of Messina, Polo Universitario dell'Annunziata, Messina, Italy.
Geraci, Claudia
  • Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, Bologna, Italy.
Schiavo, Giuseppina
  • Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, Bologna, Italy.
Utzeri, Valerio Joe
  • Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, Bologna, Italy.
Chiofalo, Vincenzo
  • Department of Veterinary Sciences, Animal Production Unit, University of Messina, Polo Universitario dell'Annunziata, Messina, Italy; Meat Research Consortium, Polo Universitario dell'Annunziata, Messina, Italy.
Fontanesi, Luca
  • Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, Bologna, Italy.

MeSH Terms

  • Animals
  • Comparative Genomic Hybridization
  • Equidae / genetics
  • Genetic Variation
  • Genome
  • High-Throughput Nucleotide Sequencing
  • Horses / genetics
  • Male
  • Polymorphism, Single Nucleotide
  • Semiconductors
  • Sequence Analysis, DNA
  • X Chromosome
  • Y Chromosome

Conflict of Interest Statement

Competing Interests: The authors have declared that no competing interests exist.

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