Data from: Genomic sequencing reveals historical, demographic and selective factors associated with the diversification of the fire-associated fungus Neurospora discreta

Gladieux P, Wilson BA, Perraudeau F, Montoya LA, Kowbel D, Hann-Soden C, Fischer M, Sylvain I, Jacobson DJ, Taylor JW

Date Published: October 8, 2015

DOI: http://dx.doi.org/10.5061/dryad.1538f

 

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Title SNPs for full set of non-redundant sequences
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Description This file contains SNPs for the 41 isolates of taxa PS4A, PS4B and PS6. Initially the dataset was comprised of 52 isolates, but after genome sequencing a "clone correction" was carried out, i.e. only one representative of groups of genome with genetic distance below 0.1 were kept in the dataset. The file used for clone correction has also been deposited on Dryad.
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Title SNPs for non-redundant European and North-American sequences
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Description This file contains SNPs for the European and North American isolates of PS4B. SNP-calling was performed independently for this set of sequences, for the full set of sequences and for the full set of non redundant sequences.
Download PS4BUSEU_HiQ.vcf (586.8 Mb)
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Title Complete genomic sequences for the full set of non-redundant sequences
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Description Genomic sequences were constructed using the genomic sequence of the reference genome and a table of SNPs.
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Title SNPs used to identify redundant sequences
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Description This files contains the SNPs that were used to identify redundant sequences. It is based on the file containing "SNPs for non-redundant European and North-American sequences", with missing data removed. It was analysed using DNADIST&NEIGHBOR programs in the PHYLIP Package, and a single representative of each clonal complex was kept in the dataset "SNPs for non-redundant European and North-American sequences" (clonal complex identified as groups of individuals with genetic distance <0.1)
Download PS4BUSEU_HiQ_woNs.phy (10.71 Mb)
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Title Mating types and Reproductive success
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Description Reproductive success of 239 crosses (478 matings). Columns represent the 16 mat A strains, and rows represent the 15 mat a strains, with isolates numbers along the row and column headings of the matrix. Numbers within matrix cells indicate the reproductive success ratings (see below) of the two reciprocal matings of the cross between the corresponding isolates (mat a isolate as the perithecial parent/mat A isolate as the perithecial parent). The matrix cells have been shaded in proportion to the reproductive success of the best mating (see Figure 5B in the corresponding publication). Additional row and column headings indicate the lineage designation (see Figure 1). Isolates P581 and TX8127 are tester strains of N. discreta sensu stricto. Categories of reproductive success, corresponding to different stages in reproductive development, from the development of perithecia, to the formation of black ascospores were scored as follows: 0 & 1 if sterile, no perithecia produced; & barren perithecia, no ostiole developed; 2 if perithecia developed ostioles, but no spores; 3 & 4 if <1% black ascospores ; & 1-15% black ascospores; 5 if 15-50% black ascospores; 6 if > 50% black ascospores.
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Title Neighbor-joining tree constructed based on a matrix F84 distance computed using the full set of sequences
Downloaded 5 times
Description Neighbor-joining tree based on F84 distance (DNADIST, PHYLIP Package). Computations were performed on the full set of SNPs and this analysis was used to identify redundant (i.e. nearly identical, or clonal) genomic sequences.
Download PS4_F84_NJ_for_figure.outtree (5.533 Kb)
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Title Maximum likelihood genealogy representing the relationships among non-redundant genomic sequences.
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Description Analyses were based on full genomic sequences (i.e. including both variant and invariant sites).
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When using this data, please cite the original publication:

Gladieux P, Wilson BA, Perraudeau F, Montoya LA, Kowbel D, Hann-Soden C, Fischer M, Sylvain I, Jacobson DJ, Taylor JW (2015) Genomic sequencing reveals historical, demographic and selective factors associated with the diversification of the fire-associated fungus Neurospora discreta. Molecular Ecology 24(22): 5657-5675. http://dx.doi.org/10.1111/mec.13417

Additionally, please cite the Dryad data package:

Gladieux P, Wilson BA, Perraudeau F, Montoya LA, Kowbel D, Hann-Soden C, Fischer M, Sylvain I, Jacobson DJ, Taylor JW (2015) Data from: Genomic sequencing reveals historical, demographic and selective factors associated with the diversification of the fire-associated fungus Neurospora discreta. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.1538f
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