Data from: A survey of genome-wide single nucleotide polymorphisms through genome re-sequencing in the Périgord black truffle (Tuber melanosporum Vittad.)

The Périgord black truffle (Tuber melanosporum Vittad.), considered a
gastronomic delicacy worldwide, is an ectomycorrhizal filamentous fungus
that is ecologically important in Mediterranean French, Italian and
Spanish woodlands. In this study, we developed a novel resource of single
nucleotide polymorphisms (SNPs) for T. melanosporum using Illumina
high-throughput resequencing. The genome from six T. melanosporum
geographical accessions was sequenced to a depth of approximately 20×.
These geographical accessions were selected from different populations
within the northern and southern regions of the geographical species
distribution. Approximately 80% of the reads for each of the six
resequenced geographical accessions mapped against the reference T.
melanosporum genome assembly, estimating the core genome size of this
organism to be approximately 110 Mbp. A total of 442 326 SNPs
corresponding to 3540 SNPs/Mbps were identified as being included in all
seven genomes. The SNPs occurred more frequently in repeated sequences
(85%), although 4501 SNPs were also identified in the coding regions of
2587 genes. Using the ratio of nonsynonymous mutations per nonsynonymous
site (pN) to synonymous mutations per synonymous site (pS) and
Tajima's D index scanning the whole genome, we were able to identify
genomic regions and genes potentially subjected to positive or purifying
selection. The SNPs identified represent a valuable resource for future
population genetics and genomics studies.