DOI: 10.5061/dryad.9gk52
title: Data from: A survey of genome-wide single nucleotide polymorphisms through genome re-sequencing in the Périgord black truffle (Tuber melanosporum Vittad.)

description: 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.
description: Tuber_melanosporum_442326SNPs_resourceThis file in gff format corresponds to the list of the 442,326 SNPs produced comparing seven Tuber melanosporum geographic accessions. The SNP calling was performed with the BWA/SAMTools and CLC Genome Workbench programs and only SNPs called by both methods were retained.Tuber_melanosporum_60507SNPs_resourceThis file in gff format corresponds to the list of the 60,507 SNPs in genomic region putatively free of selection. These SNPs were used for BEAST and maximum likelihood phylogenies. These SNPs originated from the initial 442,326 SNPs resource. SNPs in repeated sequences, gene models and genomic regions putatively under selection were not included in this file.Tuber_melanosporum_Tree_BeastThis file in newick format corresponds to the BEAST bayesian reconstruction realized with the 60,507 SNPs in region free of selection. The time estimation were obtained using a most recent common ancestor for this tree of 131,128 ± 23,098 years. This tree is presented in figure 4 of the manuscript.Tuber_melanosporum_Tree_BeastThis file in xml format has been used as input for BEAST. Bayesian phylogenetic analysis was conducted with 5,000,000 generations, a sampling for each 1,000 generations, and a burn-in value of 1,250 with BEAST version v1.7.5 using the Hasegawa-Kishino-Yano (HKY) DNA substitution model.Tuber_melanosporum_MLThis file in newick format corresponds to the maximum likelihood phylogeny realized using the default parameters of PhyML with 100 bootstrap replicates. This tree was produced using the 60,507 SNPs in genomic regions putatively free of selection. This tree is presented in figure S1 and S6.Tuber_melanosporum_genes_v1_2This file in gff format correspond to the 9,952 gene models of Tuber melanosporum considered in this analyse. Details are provided in the manuscript concerning this gene catalogue realization.