Background Leishmaniasis is one of the most important vector-borne diseases and it represents a serious world health problem affecting millions of people. High levels of Leishmania infections, affecting both humans and animals, are recognized among Italian regions. Among these, Sicily has one of the highest prevalence of Leishmania infection. Methodology/Principal Findings Seventy-eight Leishmania strains isolated from human and animal samples across Sicily, were analyzed for the polymorphic k26-gene and genotypes were assigned according to the size of the PCR products. A multilocus microsatellite typing (MLMT) approach based on the analysis of 11 independent loci was used to investigate populations structure and genetic diversity of the isolated strains. Six L. infantum reference strains were included in the analysis for comparison. Bayesian clustering analysis of microsatellite data showed that all the isolated strains clustered in two genetically distinct populations, corresponding to human and canine isolates respectively. A further subdivision was observed between the two main groups, giving a good correlation between human strains and their geographic origin, conversely canine population showed a great genetic variability diffused in the territory. Conclusions/Significance Among the 78 Leishmania isolates, K26 analysis detected 71 samples (91%) as MON-1 zymodeme, confirming it as the predominant strain in Mediterranean area and 7 human samples (9%) as non-MON-1. MLMT gives important insights into the epidemiology of leishmaniases and allows characterization of different strains to a higher resolution than possible with zymodeme typing. Two main populations presented a strong correlation respect to the different hosts, exhibiting a co-circulation of two distinct populations of L. infantum. The PLOS NEGLECTED TROPICAL DISEASES
Background Polymorphisms of the prion protein gene may influence scrapie susceptibility in small ruminants through modified protein conformation. At least 47 amino acid substitutions and 19 silent polymorphisms have been described in goat PRNP reported from several countries. The objective of this study was to investigate PRNP polymorphisms of native Ethiopian goat breeds and compare the results with other goat breeds. Results The analysis of the prion protein gene PRNP in 229 goats belonging to three of the main Ethiopian native goat breeds showed a remarkably high frequency (> 34.6%) of p.(Asn146Ser) in these breeds, a variant involved in scrapie resistance in Cyprus. In addition, two novel amino-acid substitutions p.(Gly127Ala) and p.(Thr193Ile), with frequencies ranging from 1.5 to 7.3% were detected. Both amino acids are well conserved in prion proteins (PrP) of most species and these changes have never been reported before in goats worldwide. Residue 127 is within the N–terminal domain of PrP and is probably involved in the recruitment of neural cell adhesion molecules (NCAM). Residue 193 is within the highly conserved string of 4 threonines that plays a role in determining the efficiency of prion protein conversion towards its pathological form. Conclusion Two novel coding polymorphisms and a high frequency of a scrapie protective variant indicate a high level of genetic diversity in PRNP of Ethiopian goats. This finding increases the interest in exploring PRNP polymorphisms of native goat breeds in areas where cross breeding with foreign goats has rarely occurred. Electronic supplementary material The online version of this article (10.1186/s12917-019-1870-4) contains supplementary material, which is available to authorized users.
Using next-generation sequencing, we obtained for the first time a complete mitochondrial DNA genome from a museum specimen of the extinct wolf (Canis lupus) population of the island of Sicily (Italy). Phylogenetic analyses showed that this genome, which was aligned with a number of historical and extant complete wolf and dog mtDNAs sampled worldwide, was closely related to an Italian wolf mtDNA genome (TN93 and p-distances = 0.0012), five to seven times shorter than divergence among Sicilian and any other known wolf mtDNA genomes (distance range = 0.0050 -0.0070). Sicilian and Italian haplotypes joined a basal clade belonging to the mtDNA haplogroup-2 of ancient western European wolf populations (Pilot et al. 2010). Bayesian calibration of divergence times indicated that this clade coalesced at MRCA = 13.400 years (with 95% HPD = 4000 -21.230 years). These mtDNA findings suggest that wolves probably colonized Sicily from southern Italy towards the end of the last Pleistocene glacial maximum, when the Strait of Messina was almost totally dry. Additional mtDNA and genomic data will further clarify the origin and population dynamics before the extinction of wolves in Sicily.
The most representative sheep in Sicily are Belicina, Comisana, Pinzirita, Barbaresca and the crossbred derived sheep from all this species. In this study, the allelic frequencies of the Sicilian sheep population were investigated. It currently represents the best way to determine the genetic identity and/or family even with limited amounts of sample or when the DNA is degraded. The aim of the study was to provide a reference data bank and to evaluate a microsatellite panel for pedigree analysis as suggested by the International Society for Animal Genetics (ISAG). There are various studies on European sheep, but few datasets were developed on the population of Sicilian sheep. The reference database will include allele frequencies at each locus and will determine genetic parameters for Sicilian ovine species selection. Our results indicated that Hardy Weinberg equilibrium was not always maintained. These results could be explained by a non-random mating. The database is useful to investigate the relationship, the parentage the meat traceability and in disease control programs. The standardized panels of allele frequencies represent a molecular fingerprinting characterizing the subjects with very high definition level and can be useful to control all the livestock. The parentage identification could be important for the veterinary police to investigate the theft or the animal substitutions in the Sicilian farms.
Genotyping strategies are aimed at defining the genetic profile of individuals through the identification of STRs sequences. The applied methodologies are able to ensure the traceability of the meat along the production chains and the control of the correct animal sampling on the farms. However, the discriminative capacity of alleles is studied through the establishment of the allelic frequency in the ovine population of the territory. This may depend on factors such as race, degree of inbreeding, and local selections. In the research of genetic identity in particular, it is exploited that the probability that two different individuals possess the same genetic pattern is equal to the frequency of that genotype in the population under examination and that the frequency of a genotype characterized by more loci is equal to the product of the frequencies of each single genotype (locus) observed. Therefore, we set the task of fixing and tabulating the data of the genetic profiles of the autochthonous breeds that can then be exploited for the traceability investigations of the animals, according to the application of specific algorithms. In practice, we aim to establish and create the starting point for the interpretation of all the genetic data obtained from the analysis of the Sicilian ovine population, whatever the application to do with it. The ultimate goal of this work is the elaboration of allelic panels typical of the sheep populations that represent the starting point for all genetic tests of forensic investigations. In fact, the discovery of particular alleles identify the tabulated frequency representing the genetic variability distribuited in the region. This has the effect of minimizing the identification errors that are spread in the animal population. We can state that from the analysis of allele frequencies developed by Genalex we can obtain expected heterozygosity data according to Hardy-Weinberg law and the obtained heterozygosity data typical for native breeds. All the allele frequencies were employed to create a database containing all the genotypes. These data were useful in the forensic field for the attribution of the kinships in the sheep.
20Using next-generation sequencing, we obtained for the first time a complete mitochondrial DNA 21 genome from a museum specimen of the extinct wolf (Canis lupus) population of the island of 22 Sicily (Italy). Phylogenetic analyses showed that this genome, which was aligned with a number of 23 historical and extant complete wolf and dog mtDNAs sampled worldwide, was closely related to 24 an Italian wolf mtDNA genome (TN93 and p-distances = 0.0012), five to seven times shorter than 25 divergence among Sicilian and any other known wolf mtDNA genomes (distance range = 0.0050 -26 0.0070). Sicilian and Italian haplotypes joined a basal clade belonging to the mtDNA haplogroup-2 27 of ancient western European wolf populations (Pilot et al. 2010). Bayesian calibration of 28 divergence times indicated that this clade coalesced at MRCA = 13.400 years (with 95% HPD = 29 4000 -21.230 years). These mtDNA findings suggest that wolves probably colonized Sicily from 30 southern Italy towards the end of the last Pleistocene glacial maximum, when the Strait of 31 Messina was almost totally dry. Additional mtDNA and genomic data will further clarify the origin 32 and population dynamics before the extinction of wolves in Sicily. 33 34
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