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Data have been submitted to EMBL-EBI European Nucleotide Archive (ENA) with the project accession numbers PRJEB8743 and PRJEB8744.įunding: This study was supported by University of Bologna RFO (Ricerca Fondamentale Orientata), University of Messina, Corfilcarni and PanLab Project PONa3_00166/F1 funds. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are creditedĭata Availability: Accession numbers are included in the text. Received: MaAccepted: JPublished: July 7, 2015Ĭopyright: © 2015 Bertolini et al. te Pas, Wageningen UR Livestock Research, NETHERLANDS (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. asinus and to establish monitoring systems for the conservation of donkey genetic resources.Ĭitation: Bertolini F, Scimone C, Geraci C, Schiavo G, Utzeri VJ, Chiofalo V, et al. The SNPs we identified constitute a first resource useful to describe variability at the population genomic level in E.

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. 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. Comparing Y-chromosome regions we identified variants that could be useful to track donkey paternal lineages. These regions might be evolutionally important in equids. Regions with low nucleotide divergence were identified in several autosomal chromosomes and in the whole chromosome X. This was due to the larger N50 for contigs and scaffolds of the horse genome. The number of next generation sequencing reads aligned with the EquCab2.0 horse genome was larger than those aligned with the draft donkey 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). 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. Facebook Live adds a screen-sharing extension for PCs.Few studies investigated the donkey ( Equus asinus) at the whole genome level so far. CodonCode Aligner is a program for sequence assembly and.

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