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

Payen T, Murat C, Gigant A, Morin E, De Mita S, Martin F

Date Published: February 18, 2015

DOI: http://dx.doi.org/10.5061/dryad.9gk52

 

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Title Tuber_melanosporum_442326SNPs_resource
Downloaded 11 times
Description This 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.
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Title Tuber_melanosporum_60507SNPs_resource
Downloaded 5 times
Description This 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.
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Title Tuber_melanosporum_Tree_Beast
Downloaded 8 times
Description This 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.
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Title Tuber_melanosporum_Tree_Beast
Downloaded 7 times
Description This 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.
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Title Tuber_melanosporum_ML
Downloaded 4 times
Description This 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.
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Title Tuber_melanosporum_genes_v1_2
Downloaded 7 times
Description This 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.
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When using this data, please cite the original publication:

Payen T, Murat C, Gigant A, Morin E, De Mita S, Martin F (2015) A survey of genome-wide single nucleotide polymorphisms through genome re-sequencing in the Périgord black truffle (Tuber melanosporum Vittad.). Molecular Ecology Resources 15(5): 1243–1255. http://dx.doi.org/10.1111/1755-0998.12391

Additionally, please cite the Dryad data package:

Payen T, Murat C, Gigant A, Morin E, De Mita S, Martin F (2015) Data from: A survey of genome-wide single nucleotide polymorphisms through genome re-sequencing in the Périgord black truffle (Tuber melanosporum Vittad.). Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.9gk52
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