The aims of this paper were to study the genetic diversity within and among 6 Tuber taxa, the phylogenetic relationships and the spatial distribution of truffles from the Basilicata region (southern Italy). Molecular analyses, using the internal transcribed spacer region, microsatellites, minisatellites and random amplified polymorphic loci revealed the highest expected intra-specific heterozygosity (He=0.30) in T. aestivum, followed by that of T. mesentericum (He=0.22). T. borchii (He=0.17), T. magnatum (He=0.16), T. aestivum fo. uncinatum (He=0.12) and T. brumale fo. moschatum (He=0.09) showed a lower average heterozygosity. The whole set of markers were demonstrated to be useful in clearly differentiating Tuber taxa, separating them in two distinct groups and in five sub-clusters, each corresponding to one single taxon. The first cluster (T. borchii, T. magnatum and T. brumale fo. moschatum) was more differentiated than the second one (T. aestivum, T. aestivum fo. uncinatum and T. mesentericum). T. brumale fo. moschatum was the most differentiated Tuber taxon. It was more related to the white truffles (the closely related T. borchii and T. magnatum) than to the remaining related black truffles T. aestivum and T. mesentericum. The amount of Tuber species richness was higher over the western side of Basilicata, in cold Lauretum and in Castanetum phytoclimatic Pavari’s zones. A spatial genetic structure was detected for T. aestivum, as shown by the significant correlation between geographic and genetic distances (rs=0.32; P<0.0001). Integration of molecular and geographic diversity patterns can allow the selection of sites for Tuber and Tuberrelated biodiversity conservation

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