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Bertolini F.,University of Bologna | Bertolini F.,Messina University | Scimone C.,Messina University | Geraci C.,University of Bologna | And 5 more authors.
PLoS ONE | Year: 2015

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. © 2015 Bertolini et al. 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 credited. Source


Mugnaini L.,Prophylaxis and Food Hygiene | Papini R.,Prophylaxis and Food Hygiene | Gorini G.,Environmental and Occupational Epidemiology Unit | Passantino A.,Polo Universitario dellAnnunziata | And 2 more authors.
Revue de Medecine Veterinaire | Year: 2012

The pattern of endoparasite infections was examined in 273 cats (181 owned cats, 54 sheltered cats, and 28 stray cats from colonies) by combining results of different diagnostic techniques. Overall, 26.4% of cats harboured one (for 86.1% of positive cats) or more endoparasites including Toxocara cati (12.1%), Cystoisospora felis (2.9%), Aelurostrongylus abstrusus (2.2%), C. felis/T. cati and Cystoisospora rivolta (1.8% each), Ancylostoma tubaeforme (1.1%), C. rivolta/T. cati, Dipylidium caninum, Eucoleus aerophilus and Toxascaris leonina (0.7% each), A. abstrusus/D. caninum/T. cati, A. tubaeforme/ T. cati, C. felis/D. caninum, and Cryptosporidium felis (0.4% each). Tritrichomonas foetus was not detected. In univariate analysis, predictive factors of endoparasitism included being male, intact, less than 1-year-old, stray or owned-outdoor, untreated, and fed occasionally with homemade food. Multivariate analysis showed that males were 4.25 times more likely to be infected if they were less than 1-year-old and 3.21 times if they did not receive periodical antiparasite treatments while females were 10.43 more likely to be infected if showing intestinal or respiratory clinical signs. These data may be of importance for veterinary practitioners to evaluate the occurrence of endoparasitism in cats. Source


Gaglio G.,Polo Universitario dellAnnunziata | Gaglio G.,University of Bristol | Allen S.,Gower Bird Hospital | Bowden L.,University of Bristol | And 2 more authors.
European Journal of Wildlife Research | Year: 2010

Seventy-four European hedgehogs (Erinaceus europaeus) that had died in wildlife rehabilitation centres were dissected and their parasite burdens documented. Overall parasite prevalence was 91%, and a total of six helminth species were isolated: five nematodes (Crenosoma striatum, Eucoleus aerophilus, Capillaria erinacei, Capillaria ovoreticulata and Capillaria spp.), one trematode (Brachylaemus erinacei) and one acanthocephalan (Oliganthorhynchus erinacei). The tick Ixodes hexagonus and flea Archeopsylla erinacei were also collected. The effect of parasite infection on body condition was assessed by correlation of burdens with the residuals of weight-skeletal length regression. Tick presence was positively related to body condition; for other parasites, no significant relationship was found. Faecal egg or larval count was closely correlated with adult parasite burden for C. striatum and Capillaria/Eucoleus spp., but not for other species. Coprological analysis should therefore be useful for in vivo studies of nematode parasite infection in hedgehogs. The epidemiology of parasites in hedgehogs and their possible role in recent population declines are discussed. © 2010 Springer-Verlag. Source


Bertolini F.,University of Bologna | Ghionda M.C.,University of Bologna | Ghionda M.C.,Messina University | D'Alessandro E.,Messina University | And 4 more authors.
PLoS ONE | Year: 2015

The identification of the species of origin ofmeat and meat products is an important issue to prevent and detect frauds that might have economic, ethical and health implications. In this paper we evaluated the potential of the next generation semiconductor based sequencing technology (Ion Torrent Personal Genome Machine) for the identification of DNA from meat species (pig, horse, cattle, sheep, rabbit, chicken, turkey, pheasant, duck, goose and pigeon) as well as from human and rat in DNA mixtures through the sequencing of PCR products obtained from different couples of universal primers that amplify 12S and 16S rRNA mitochondrial DNA genes. Six libraries were produced including PCR products obtained separately from 13 species or fromDNA mixtures containing DNA fromall species or only avian or only mammalian species at equimolar concentration or at 1:10 or 1:50 ratios for pig and horse DNA. Sequencing obtained a total of 33,294,511 called nucleotides of which 29,109,688 with Q20 (87.43%) in a total of 215,944 reads. Different alignment algorithms were used to assign the species based on sequence data. Error rate calculated after confirmation of the obtained sequences by Sanger sequencing ranged from0.0003 to 0.02 for the different species. Correlation about the number of reads per species between different libraries was high for mammalian species (0.97) and lower for avian species (0.70). PCR competition limited the efficiency of amplification and sequencing for avian species for some primer pairs. Detection of low level of pig and horse DNA was possible with reads obtained from different primer pairs. The sequencing of the products obtained from different universal PCR primers could be a useful strategy to overcome potential problems of amplification. Based on these results, the Ion Torrent technology can be applied for the identification of meat species in DNA mixtures. © 2015 Bertolini et al. Source


Moravec F.,Academy of Sciences of the Czech Republic | Gaglio G.,Polo Universitario dellAnnunziata | Giannetto S.,Polo Universitario dellAnnunziata | Marino F.,Polo Universitario dellAnnunziata
Parasitology Research | Year: 2010

A new nematode species, Philometra spicarae sp. n. (Philometridae), is described from a gravid female found in the abdominal cavity of spicarel, Spicara smaris (Linnaeus) (Centracanthidae, Perciformes), from the Ionian Sea off Sicily, Italy. The new species differs from most other Philometra spp. parasitic in the abdominal cavity of marine fishes by the oesophagus without an anterior inflation, resembling thus only Philometra cheilopogoni Mordvinova, 1986 and Philometra justinei Moravec, Ternengo and Levron, 2006; these two species can be differentiated from P. spicarae by the relative length of the oesophagus to body length (0.6-0.8% vs. 6%) and some other features. From the gonad-infecting species Philometra filiformis (Stossich, 1896), a parasite of Pagellus erythrinus (Linnaeus), P. spicarae differs mainly in having a conspicuously long (1.4 mm) intestinal ligament. It is the first nominal philometrid species described from the fish of the family Centracanthidae. © 2010 Springer-Verlag. Source

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